[Yt-svn] yt-commit r559 - in trunk/doc: . build/doctrees build/doctrees/cookbook build/doctrees/modules/lagos build/doctrees/tutorial build/html build/html/_images build/html/_sources build/html/_sources/cookbook build/html/_sources/tutorial build/html/_static build/html/cookbook build/html/extending build/html/modules/lagos build/html/modules/raven build/html/modules/reason build/html/tutorial source source/.static source/.templates source/_images source/cookbook source/static source/tutorial
mturk at wrangler.dreamhost.com
mturk at wrangler.dreamhost.com
Mon Jun 16 12:45:33 PDT 2008
Author: mturk
Date: Mon Jun 16 12:45:22 2008
New Revision: 559
URL: http://yt.spacepope.org/changeset/559
Log:
Another huge documentation commit. Still a ways to go, but it is coming
together a bit.
Added:
trunk/doc/build/doctrees/cookbook/analyzing_data.doctree (contents, props changed)
trunk/doc/build/doctrees/cookbook/extracting_data.doctree (contents, props changed)
trunk/doc/build/doctrees/cookbook/grouping_data.doctree (contents, props changed)
trunk/doc/build/doctrees/cookbook/making_movies.doctree (contents, props changed)
trunk/doc/build/doctrees/cookbook/making_simple_plots.doctree (contents, props changed)
trunk/doc/build/doctrees/cookbook/making_timeseries_plots.doctree (contents, props changed)
trunk/doc/build/html/_images/
trunk/doc/build/html/_images/example_3dphase.png (contents, props changed)
trunk/doc/build/html/_sources/cookbook/analyzing_data.txt
trunk/doc/build/html/_sources/cookbook/extracting_data.txt
trunk/doc/build/html/_sources/cookbook/grouping_data.txt
trunk/doc/build/html/_sources/cookbook/making_movies.txt
trunk/doc/build/html/_sources/cookbook/making_simple_plots.txt
trunk/doc/build/html/_sources/cookbook/making_timeseries_plots.txt
trunk/doc/build/html/_static/override.css
trunk/doc/build/html/cookbook/analyzing_data.html
trunk/doc/build/html/cookbook/extracting_data.html
trunk/doc/build/html/cookbook/grouping_data.html
trunk/doc/build/html/cookbook/making_movies.html
trunk/doc/build/html/cookbook/making_simple_plots.html
trunk/doc/build/html/cookbook/making_timeseries_plots.html
trunk/doc/source/.static/override.css
trunk/doc/source/_images/
trunk/doc/source/_images/example_3dphase.png (contents, props changed)
trunk/doc/source/_images/example_cuttingplane.png (contents, props changed)
trunk/doc/source/_images/example_phaseplot.png (contents, props changed)
trunk/doc/source/cookbook/analyzing_data.rst
trunk/doc/source/cookbook/extracting_data.rst
trunk/doc/source/cookbook/grouping_data.rst
trunk/doc/source/cookbook/making_movies.rst
trunk/doc/source/cookbook/making_simple_plots.rst
trunk/doc/source/cookbook/making_timeseries_plots.rst
trunk/doc/source/static/
trunk/doc/source/static/default.css
trunk/doc/wipe_svn.sh
Removed:
trunk/doc/build/doctrees/tutorial/derived_quantities.doctree
trunk/doc/build/html/_sources/tutorial/derived_quantities.txt
trunk/doc/build/html/tutorial/derived_quantities.html
trunk/doc/source/tutorial/derived_quantities.rst
Modified:
trunk/doc/README
trunk/doc/build/doctrees/environment.pickle
trunk/doc/build/doctrees/faq.doctree
trunk/doc/build/doctrees/modules/lagos/basedatatypes.doctree
trunk/doc/build/doctrees/modules/lagos/outputandhierarchy.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/html/_sources/faq.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/cookbook/index.html
trunk/doc/build/html/extending/analyzing_in_parallel.html
trunk/doc/build/html/extending/creating_datatypes.html
trunk/doc/build/html/extending/creating_derived_fields.html
trunk/doc/build/html/extending/creating_derived_quantities.html
trunk/doc/build/html/extending/index.html
trunk/doc/build/html/extending/plugin_file.html
trunk/doc/build/html/extending/running_fortran_routines.html
trunk/doc/build/html/extending/using_the_interpreter.html
trunk/doc/build/html/extending/writing_scripts.html
trunk/doc/build/html/faq.html
trunk/doc/build/html/genindex.html
trunk/doc/build/html/index.html
trunk/doc/build/html/intro.html
trunk/doc/build/html/modindex.html
trunk/doc/build/html/modules/lagos/basedatatypes.html
trunk/doc/build/html/modules/lagos/contours.html
trunk/doc/build/html/modules/lagos/index.html
trunk/doc/build/html/modules/lagos/outputandhierarchy.html
trunk/doc/build/html/modules/lagos/profiles.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/example_script.html
trunk/doc/build/html/tutorial/getting_started.html
trunk/doc/build/html/tutorial/index.html
trunk/doc/build/html/tutorial/profiles.html
trunk/doc/build/html/tutorial/projections.html
trunk/doc/source/.templates/layout.html
trunk/doc/source/conf.py
trunk/doc/source/faq.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
Modified: trunk/doc/README
==============================================================================
--- trunk/doc/README (original)
+++ trunk/doc/README Mon Jun 16 12:45:22 2008
@@ -7,4 +7,4 @@
All of the pre-built HTML files, accessible with any web browser, are available
in the build/ directory, as well as at:
-http://yt.spacepope.org/doc/index.html
+http://yt.enzotools.org/doc/index.html
Added: trunk/doc/build/doctrees/cookbook/analyzing_data.doctree
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Added: trunk/doc/build/doctrees/cookbook/extracting_data.doctree
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Added: trunk/doc/build/doctrees/cookbook/grouping_data.doctree
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Added: trunk/doc/build/doctrees/cookbook/making_movies.doctree
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Added: trunk/doc/build/doctrees/cookbook/making_simple_plots.doctree
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Added: trunk/doc/build/doctrees/cookbook/making_timeseries_plots.doctree
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Modified: trunk/doc/build/doctrees/environment.pickle
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Modified: trunk/doc/build/doctrees/faq.doctree
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Modified: trunk/doc/build/doctrees/modules/lagos/basedatatypes.doctree
==============================================================================
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Modified: trunk/doc/build/doctrees/modules/lagos/outputandhierarchy.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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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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Added: trunk/doc/build/html/_images/example_3dphase.png
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Added: trunk/doc/build/html/_sources/cookbook/analyzing_data.txt
==============================================================================
Added: trunk/doc/build/html/_sources/cookbook/extracting_data.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/cookbook/extracting_data.txt Mon Jun 16 12:45:22 2008
@@ -0,0 +1,26 @@
+Extracting Data
+===============
+
+Oftentimes you will want to export data from yt to plot in another plotting
+package, or to compare against another set of data elsewhere. (Although, note
+should be made that ever effort has been made to make yt into a
+publication-quality plotter.)
+
+Data objects all have the :meth:`write_out` method, which accepts a field
+list and a filename. This will dump to text.
+
+However, if you have `PyTables <http://www.pytables.org/>`_ installed, you can
+also export things in a different way: ::
+
+ >>> cube = pf.h.smoothed_covering_grid(3, left_edge=[0.0,0.0,0.0],
+ ... right_edge=[1.0,1.0,1.0],
+ ... dims=[512,512,512],
+ ... fields=["Density"])
+ >>> f = tables.openFile("my_cube.h5","w")
+ >>> f.createArray("/","my_cube_density", cube["Density"])
+ >>> f.close()
+
+This will generate an HDF5 file with the "Density" array from our smoothed cube
+at the root node, and called "my_cube_density". With PyTables you can nest
+these, set attributes, and access the data through any application that can
+read HDF5.
Added: trunk/doc/build/html/_sources/cookbook/grouping_data.txt
==============================================================================
Added: trunk/doc/build/html/_sources/cookbook/making_movies.txt
==============================================================================
Added: trunk/doc/build/html/_sources/cookbook/making_simple_plots.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/cookbook/making_simple_plots.txt Mon Jun 16 12:45:22 2008
@@ -0,0 +1,91 @@
+Making Simple Plots
+===================
+
+Single Width Plots
+------------------
+
+Making plots can be considered one of the simplest things to do in yt, and at
+its most primitive you can simply declare which plots to make.
+
+The following recipe opens the parameter file, creates a 'collection' of plots,
+adds a few slices, and then saves it at a fixed width.
+
+.. code-block:: python
+
+ pf = lagos.EnzoStaticOutput("my_data/my_data0001")
+ pc = raven.PlotCollection(pf)
+ pc.add_slice("Density",0)
+ pc.add_slice("Density",1)
+ pc.add_slice("Density",2)
+ pc.set_width(100.0,'kpc')
+ pc.save("my_data0001_100kpc")
+
+Multiple Fields Single Width
+----------------------------
+
+The 'save' command encodes the name of the field into the filename. It is more
+efficient to 'switch' a field than to add a new slice with a different field.
+
+.. code-block:: python
+
+ fields = ["Density", "Temperature", "x-velocity"]
+ pf = lagos.EnzoStaticOutput("my_data/my_data0001")
+ pc = raven.PlotCollection(pf)
+ pc.add_slice(fields[0],0)
+ pc.add_slice(fields[0],1)
+ pc.add_slice(fields[0],2)
+ pc.set_width(100.0,'kpc')
+ for field in fields:
+ pc.switch_field(field)
+ pc.save("my_data0001_100kpc")
+
+Single Field Multiple Widths
+----------------------------
+
+We can zoom in on our slice very easily, and we can define it to do that and
+vary units, too, thus ensuring we have a consistent set of plots.
+
+.. note::
+ We do some fancy footwork here with the creation of *my_pairs* but it is an
+ idiom that can be applied elsewhere.
+
+.. code-block:: python
+
+ widths = [1000.0, 100.0, 10.0, 1.0]
+ units = ['mpc','kpc','pc','au']
+ my_pairs = [ (w,u) for u in units for w in widths ]
+
+ pf = lagos.EnzoStaticOutput("my_data/my_data0001")
+ pc = raven.PlotCollection(pf)
+ pc.add_slice("Density",0)
+ pc.add_slice("Density",1)
+ pc.add_slice("Density",2)
+ for w, u in my_pairs:
+ pc.set_width(w,u)
+ pc.save("my_data0001_%05i%s" % (w, u))
+
+Multiple Fields Multiple Widths
+-------------------------------
+
+Because of the way the slices are created and the fields handled, we set our
+outer loop to be over the field and the inner loop to be over the widths.
+
+.. code-block:: python
+
+ fields = ["Density", "Temperature", "x-velocity"]
+ widths = [1000.0, 100.0, 10.0, 1.0]
+ units = ['mpc','kpc','pc','au']
+ my_pairs = [ (w,u) for u in units for w in widths ]
+
+ pf = lagos.EnzoStaticOutput("my_data/my_data0001")
+ pc = raven.PlotCollection(pf)
+ pc.add_slice(fields[0],0)
+ pc.add_slice(fields[0],1)
+ pc.add_slice(fields[0],2)
+ for field in fields:
+ pc.switch_field(field)
+ for w, u in my_pairs:
+ pc.set_width(w,u)
+ pc.save("my_data0001_%05i%s" % (w, u))
+
+
Added: trunk/doc/build/html/_sources/cookbook/making_timeseries_plots.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/cookbook/making_timeseries_plots.txt Mon Jun 16 12:45:22 2008
@@ -0,0 +1,54 @@
+Making Timeseries Plots
+=======================
+
+I don't think anyone will argue that timeseries data is important. It is
+possible to create it with yt; however, a few things should be noted.
+
+Python is notorious for leaking memory via circular references -- if you
+have a variable *var1* that references variable *var2*, when one is deleted, is
+the other? Efforts have been made to identify and remove all leaking
+references, but if references are created in your code that generates the
+timeseries data, you may find that more memory is used than is desired.
+
+The process of generating time series data is fairly simple: you iterate over
+the datasets, and generate a value for each. ::
+
+ >>> max_rho = []
+ >>> max_pos = []
+ >>> times = []
+ >>> for i in range(30):
+ ... pf = lagos.EnzoStaticOutput("my_output%04i" % (i))
+ ... v, c = pf.h.find_max("Density")
+ ... max_rho.append(v)
+ ... max_pos.append(c)
+ ... times.append(pf["CosmologyCurrentTime"] * pf["years"])
+ >>> pylab.loglog(times, max_rho)
+ >>> pylab.clf()
+
+You could also imagine doing a time-evolution of an averaged quantity::
+
+ >>> avg_T = []
+ >>> times = []
+ >>> for i in range(30):
+ ... pf = lagos.EnzoStaticOutput("my_output%04i" % (i))
+ ... v, c = pf.h.find_max("Density")
+ ... sp = pf.h.sphere(c, 10.0/pf['kpc'])
+ ... avg_T.append(sp.quantities["WeightedAverageQuantity"]("Temperature",
+ ... "CellMassMsun")
+ ... times.append(pf["CosmologyCurrentTime"] * pf["years"])
+ >>> pylab.loglog(times, avg_T)
+
+At this point, you can also write out the data to a file and plot it in another
+plotting package: ::
+
+ >>> f = open("my_data.dat", "w")
+ >>> for i in range(len(times)):
+ ... f.write("%0.5e %0.5e\n" % (times[i], avg_T[i]))
+
+More complicated analysis can be done as well; :class:`PlotCollections`
+created, slices made, etc.
+
+The package :mod:`fido` inside of yt is also available, but it is not
+well-documented. It will store information about outputs, associated with a
+given run, and you can iterate over those. This is altogether a simpler
+process, but it is not resilient against data movement.
Modified: trunk/doc/build/html/_sources/faq.txt
==============================================================================
--- trunk/doc/build/html/_sources/faq.txt (original)
+++ trunk/doc/build/html/_sources/faq.txt Mon Jun 16 12:45:22 2008
@@ -80,7 +80,7 @@
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/>`_.
+first!) or attach them to a ticket at `<http://yt.enzotools.org/>`_.
.. _axis-specification:
@@ -95,4 +95,4 @@
---------------------------
I've set up a ``yt-users`` mailing list. There's more information about it
-at the `yt homepage <http://yt.spacepope.org>`_.
+at the `yt homepage <http://yt.enzotools.org>`_.
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 Jun 16 12:45:22 2008
@@ -64,3 +64,29 @@
Grid Collections
----------------
+
+Disks
+-----
+
+Clumps
+------
+
+Derived Quantities
+==================
+
+Associated with a given data object, one can imagine various quantities being
+described. Several of these are already included in yt, and more can be added.
+To access a derived quantity, the property 'quantities' is available in a given
+data object. It acts as a dictionary, returning callable functions.::
+
+ >>> L_vec = gal1_region.quantities["AngularMomentumVector"]()
+ >>> com = gal1_region.quantities["CenterOfMass"]()
+ >>> avg_T = gal1_region.quantities["WeightedAverageQuantity"]("Temperature", \
+ ... "CellMassMsun")
+
+All derived quantities accept the parameter :keyword:`lazy_reader`, which
+tells the function to attempt to operate in a memory-conservative fashion --
+reading and then flushing the data back to disk. This is not possible for all
+functions, notably the :func:`IsBound` function, which checks for
+gravitationally-bound status.
+
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 Jun 16 12:45:22 2008
@@ -57,4 +57,4 @@
interface, including cutting planes and projections. (More on those later!)::
>>> pc.add_projection("Temperature", 0, weight_field="CellMass")
- >>> pc.add_threephase_sphere(1.0, 'pc', ["Density","Temperature","H2I_Fraction"])
+ >>> pc.add_phase_sphere(1.0, 'pc', ["Density","Temperature","H2I_Fraction"])
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 Jun 16 12:45:22 2008
@@ -3,14 +3,6 @@
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.
-
-.. index:: derivedfield, indices
-
Derived Fields and Indices
--------------------------
@@ -32,6 +24,10 @@
>>> print my_grid["Density"][0,:,4]
>>> print my_grid["Density"][0,2:4,4]
+The first will return to us everything where the x index is zero and the z
+index is four. The second will return the same, except restrict the return to
+only between indices 2 and 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
@@ -63,11 +59,18 @@
used implicity with plotting (more on that later) and not very often from
the interpreter.
-Data Regions
-------------
+Boxes
+-----
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.::
>>> my_region = a.h.region([0.5,0.5,0.5], [0.0,0.0,0.0], [1.0,1.0,1.0])
+
+This data object will respect a fixed protocol, as will all the 3D objects.
+You ask it for a field, and it returns that field: ::
+
+ >>> my_region["Density"]
+
+We'll talk more about which fields are available in the next section.
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 Jun 16 12:45:22 2008
@@ -19,7 +19,7 @@
Defining Simple Fields
----------------------
-There are LOTS! Not only that, but you can set up your own fields, too,
+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.::
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 Jun 16 12:45:22 2008
@@ -24,22 +24,35 @@
>>> import yt.lagos as lagos
+The :mod:`yt.lagos` module is now in our namespace and called :mod:`lagos`; you
+can import it as whatever you like, but we'll stick with that for the remainder
+of the tutorial. Let's move on to opening an output.
+
.. index:: hierarchy
The Hierarchy
-------------
-We first instantiate a StaticOutput. This is a pretty simple process - lagos
+We first instantiate a StaticOutput, which is a single disk-written timestep of
+the simulation This is a pretty simple process - :mod:`lagos`
will grab the parameter file that you give it, parse it, set up some handy
units, and then return control to you.::
- >>> a = lagos.EnzoStaticOutput("/Users/matthewturk/Research/data/DataDir0036/DataDump0036")
+ >>> a = lagos.EnzoStaticOutput("my_data0001.dir/my_data0001")
But what good is just a parameter file? What we really want is to be able to
manipulate the grids, and all the fields stored in those grids. Fortunately,
we can access the hierarchy as either 'hierarchy' or 'h'.
-Let's start out by finding the location of the maximum Density.
+
+The 'h' property will instantiate an :class:`EnzoHierarchy` object, which
+posseses information about the grids in a given output, as well as their
+spatial relationships to each other. Furthermore, :mod:`yt` will store
+commonly-used and expensive-to-generate data in an HDF5 file associated with
+that object -- things like projections, 3D phase profiles, and so on.
+
+All of the data-handling we want to do will be mediated by the hierarchy file;
+so let's start out by finding the location of the maximum Density.
Note that here we use an inline-unpacking -- find_max returns two values,
packed into a tuple, so we manually unpack them right here.::
@@ -49,13 +62,18 @@
.. index:: Grid, 3ddata;grid
+Now we know where the maximum density is located, and what it is. This is a
+pretty simple process, and we will use it later to center spheres and boxes and
+disks on the point of maximum density.
+
+
The Grids
---------
The hierarchy object has some interesting methods that let us access the data
in different ways. Let's start by looking at the grids. ::
- >>> my_grid = a.h.grids[0] # The root grid
+ >>> my_grid = a.h.grids[0] # The first grid in the hierarchy
>>> print my_grid.dx, my_grid.ActiveDimensions # Some of the attributes
@@ -64,7 +82,6 @@
>>> print dir(my_grid)
-
In general, a method or property that begins with '_' is not meant to be
called directly, and '__' means that it definitely shouldn't be called by an
external process.
@@ -74,4 +91,12 @@
>>> print my_grid["Density"]*my_grid["Temperature"]
+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. In the
+next section we'll take about the difference between a native field and a
+derived field.
+.. index:: derivedfield, indices
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 Jun 16 12:45:22 2008
@@ -18,5 +18,4 @@
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 Jun 16 12:45:22 2008
@@ -2,7 +2,7 @@
========
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,
+of one or more variables, along one, two or three different dimensions. For example,
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.
@@ -46,6 +46,9 @@
>>> pylab.ylabel(r"$\rm{Density} (\rm{g}/\rm{cm}^3)$")
>>> pylab.savefig("my_profile.png")
+Note that we manually plot it, but :mod:`raven` also includes an automated
+plotting method for obtaining and displaying radial profiles.
+
Two-Dimensional Profiles
------------------------
@@ -57,3 +60,59 @@
>>> prof2d.add_fields("CellVolume", weight=None)
>>> pylab.pcolormesh(prof2d["Density"], prof2d["Temperature"],
... prof2d["CellVolume"].transpose())
+
+Again, we have manually plotted this, but an automated plotter is available.::
+
+ >>> pc = raven.PlotCollection(a)
+ >>> pc.add_phase_object(sphere, ["Density", "Temperature", "x-velocity"],
+ ... 16, True, (1e-32, 1e-24),
+ ... 16, True, (1e2, 1e5), lazy_reader=True)
+
+The API is slightly different here, but it will accept any object (a sphere in
+our case) and generate the profile based on the arguments. If you simply want
+a sphere, you can ask for that and the sphere will be generated as well -- and
+the function will automatically generate the bounds. (Although, keep in mind,
+if you do not supply bounds it will have to read the data into memory, which
+means you are no longer able to use the :keyword:`lazy_reader` functionality.
+This will change in future versions.) ::
+
+
+ >>> pc.add_phase_sphere(0.1, 'kpc', ["Density", "Temperature", "x-velocity"])
+
+Three-Dimensional Profiles
+--------------------------
+
+.. image:: ../_images/example_3dphase.png
+ :align: left
+ :width: 250
+
+If you have the `S2PLOT <http://astronomy.swin.edu.au/s2plot/index.php?title=S2PLOT>`_
+bindings installed, you can visualize three-dimensional profiles with yt. The
+API is nearly identical to that used to generate the lower-dimensionality
+profiles. ::
+
+ >>> prof = lagos.BinnedProfile3D(sphere,
+ ... 128, "Density", extrema[0][0], extrema[0][1], True,
+ ... 128, "Temperature", extrema[1][0], extrema[1][1], True,
+ ... 128, "z-velocity", extrema[2][0], extrema[2][1], True,
+ ... lazy_reader=True)
+ >>> prof.add_fields("CellMassMsun", None)
+
+I've wrapped the bounds into the variable *extrema*, to make it more clear.
+Once you have this profile, you can plot it with S2PLOT by calling initializing
+a 3D plot and calling :func:`run`. ::
+
+ >>> vrc = raven.VolumeRendering3DProfile(k, "CellMassMsun", amax=1.0)
+ >>> vrc.run()
+
+They can be generated anywhere -- and serialized -- so if you want to generate
+them on a remote machine and use a local-machine for display, you only have to
+call :func:`store` and then initialize, instead of the standard
+:class:`BinnedProfile3D`, :class:`StoredBinnedProfile3D`. ::
+
+ >>> prof.store_profile('MyProfile')
+ >>> new_prof = lagos.StoredBinnedProfile3D(a, 'MyProfile')
+
+The retrieved profile is static, and new data cannot be added. However, it
+becomes useful in the likely circumstance that your data is stored on a machine
+on which is inconvenient to do OpenGL-based data exploration.
Added: trunk/doc/build/html/_static/override.css
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_static/override.css Mon Jun 16 12:45:22 2008
@@ -0,0 +1,3 @@
+.documentwrapper {
+ background: #000000;
+}
Added: trunk/doc/build/html/cookbook/analyzing_data.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/cookbook/analyzing_data.html Mon Jun 16 12:45:22 2008
@@ -0,0 +1,85 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title> — yt v0.3-pre 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-pre'
+ };
+ </script>
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\ No newline at end of file
Added: trunk/doc/build/html/cookbook/extracting_data.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/cookbook/extracting_data.html Mon Jun 16 12:45:22 2008
@@ -0,0 +1,113 @@
+<!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>Extracting Data — yt v0.3-pre 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">
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+ URL_ROOT: '../',
+ VERSION: '0.3-pre'
+ };
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+
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+ </ul>
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+ <div class="body">
+
+
+ <div class="section">
+<h1 id="extracting-data">Extracting Data<a class="headerlink" href="#extracting-data" title="Permalink to this headline">¶</a></h1>
+<p>Oftentimes you will want to export data from yt to plot in another plotting
+package, or to compare against another set of data elsewhere. (Although, note
+should be made that ever effort has been made to make yt into a
+publication-quality plotter.)</p>
+<p>Data objects all have the <tt class="xref docutils literal"><span class="pre">write_out()</span></tt> method, which accepts a field
+list and a filename. This will dump to text.</p>
+<p>However, if you have <a class="reference" href="http://www.pytables.org/">PyTables</a> installed, you can
+also export things in a different way:</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">cube</span> <span class="o">=</span> <span class="n">pf</span><span class="o">.</span><span class="n">h</span><span class="o">.</span><span class="n">smoothed_covering_grid</span><span class="p">(</span><span class="mf">3</span><span class="p">,</span> <span class="n">left_edge</span><span class="o">=</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="gp">... </span> <span class="n">right_edge</span><span class="o">=</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>
+<span class="gp">... </span> <span class="n">dims</span><span class="o">=</span><span class="p">[</span><span class="mf">512</span><span class="p">,</span><span class="mf">512</span><span class="p">,</span><span class="mf">512</span><span class="p">],</span>
+<span class="gp">... </span> <span class="n">fields</span><span class="o">=</span><span class="p">[</span><span class="s">"Density"</span><span class="p">])</span>
+<span class="gp">>>> </span><span class="n">f</span> <span class="o">=</span> <span class="n">tables</span><span class="o">.</span><span class="n">openFile</span><span class="p">(</span><span class="s">"my_cube.h5"</span><span class="p">,</span><span class="s">"w"</span><span class="p">)</span>
+<span class="gp">>>> </span><span class="n">f</span><span class="o">.</span><span class="n">createArray</span><span class="p">(</span><span class="s">"/"</span><span class="p">,</span><span class="s">"my_cube_density"</span><span class="p">,</span> <span class="n">cube</span><span class="p">[</span><span class="s">"Density"</span><span class="p">])</span>
+<span class="gp">>>> </span><span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</pre></div>
+<p>This will generate an HDF5 file with the “Density” array from our smoothed cube
+at the root node, and called “my_cube_density”. With PyTables you can nest
+these, set attributes, and access the data through any application that can
+read HDF5.</p>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="making_timeseries_plots.html" title="previous chapter">Making Timeseries Plots</a></p>
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+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
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+</html>
\ No newline at end of file
Added: trunk/doc/build/html/cookbook/grouping_data.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/cookbook/grouping_data.html Mon Jun 16 12:45:22 2008
@@ -0,0 +1,80 @@
+<!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-pre 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-pre'
+ };
+ </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>
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+ <link rel="top" title="yt v0.3-pre documentation" href="../index.html" />
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+ <ul class="this-page-menu">
+ <li><a href="../_sources/cookbook/grouping_data.txt">Show Source</a></li>
+ </ul>
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
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+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
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+ </div>
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+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
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+ Last updated on Jun 16, 2008.
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+</html>
\ No newline at end of file
Modified: trunk/doc/build/html/cookbook/index.html
==============================================================================
--- trunk/doc/build/html/cookbook/index.html (original)
+++ trunk/doc/build/html/cookbook/index.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Cookbook — yt v0.3 documentation</title>
+ <title>Cookbook — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre 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>
@@ -29,9 +29,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -66,9 +66,11 @@
</ul>
<ul class="simple">
</ul>
-<ul class="simple">
+<ul>
+<li><a class="reference" href="making_timeseries_plots.html">Making Timeseries Plots</a></li>
</ul>
-<ul class="simple">
+<ul>
+<li><a class="reference" href="extracting_data.html">Extracting Data</a></li>
</ul>
</div>
@@ -103,15 +105,15 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
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<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 14, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Added: trunk/doc/build/html/cookbook/making_movies.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/cookbook/making_movies.html Mon Jun 16 12:45:22 2008
@@ -0,0 +1,85 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ <div class="section">
+<h1 id="making-simple-plots">Making Simple Plots<a class="headerlink" href="#making-simple-plots" title="Permalink to this headline">¶</a></h1>
+<div class="section">
+<h2 id="single-width-plots">Single Width Plots<a class="headerlink" href="#single-width-plots" title="Permalink to this headline">¶</a></h2>
+<p>Making plots can be considered one of the simplest things to do in yt, and at
+its most primitive you can simply declare which plots to make.</p>
+<p>The following recipe opens the parameter file, creates a ‘collection’ of plots,
+adds a few slices, and then saves it at a fixed width.</p>
+<div class="highlight"><pre><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="s">"my_data/my_data0001"</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="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="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="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="n">pc</span><span class="o">.</span><span class="n">set_width</span><span class="p">(</span><span class="mf">100.0</span><span class="p">,</span><span class="s">'kpc'</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">"my_data0001_100kpc"</span><span class="p">)</span>
+</pre></div>
+</div>
+<div class="section">
+<h2 id="multiple-fields-single-width">Multiple Fields Single Width<a class="headerlink" href="#multiple-fields-single-width" title="Permalink to this headline">¶</a></h2>
+<p>The ‘save’ command encodes the name of the field into the filename. It is more
+efficient to ‘switch’ a field than to add a new slice with a different field.</p>
+<div class="highlight"><pre><span class="n">fields</span> <span class="o">=</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">"x-velocity"</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="s">"my_data/my_data0001"</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="n">pc</span><span class="o">.</span><span class="n">add_slice</span><span class="p">(</span><span class="n">fields</span><span class="p">[</span><span class="mf">0</span><span class="p">],</span><span class="mf">0</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="n">fields</span><span class="p">[</span><span class="mf">0</span><span class="p">],</span><span class="mf">1</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="n">fields</span><span class="p">[</span><span class="mf">0</span><span class="p">],</span><span class="mf">2</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="mf">100.0</span><span class="p">,</span><span class="s">'kpc'</span><span class="p">)</span>
+<span class="k">for</span> <span class="n">field</span> <span class="ow">in</span> <span class="n">fields</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="n">pc</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"my_data0001_100kpc"</span><span class="p">)</span>
+</pre></div>
+</div>
+<div class="section">
+<h2 id="single-field-multiple-widths">Single Field Multiple Widths<a class="headerlink" href="#single-field-multiple-widths" title="Permalink to this headline">¶</a></h2>
+<p>We can zoom in on our slice very easily, and we can define it to do that and
+vary units, too, thus ensuring we have a consistent set of plots.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">We do some fancy footwork here with the creation of <em>my_pairs</em> but it is an
+idiom that can be applied elsewhere.</p>
+</div>
+<div class="highlight"><pre><span class="n">widths</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">units</span> <span class="o">=</span> <span class="p">[</span><span class="s">'mpc'</span><span class="p">,</span><span class="s">'kpc'</span><span class="p">,</span><span class="s">'pc'</span><span class="p">,</span><span class="s">'au'</span><span class="p">]</span>
+<span class="n">my_pairs</span> <span class="o">=</span> <span class="p">[</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="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">units</span> <span class="k">for</span> <span class="n">w</span> <span class="ow">in</span> <span class="n">widths</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="s">"my_data/my_data0001"</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="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="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="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="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_pairs</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">"my_data0001_</span><span class="si">%05i%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">w</span><span class="p">,</span> <span class="n">u</span><span class="p">))</span>
+</pre></div>
+</div>
+<div class="section">
+<h2 id="multiple-fields-multiple-widths">Multiple Fields Multiple Widths<a class="headerlink" href="#multiple-fields-multiple-widths" title="Permalink to this headline">¶</a></h2>
+<p>Because of the way the slices are created and the fields handled, we set our
+outer loop to be over the field and the inner loop to be over the widths.</p>
+<div class="highlight"><pre><span class="n">fields</span> <span class="o">=</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">"x-velocity"</span><span class="p">]</span>
+<span class="n">widths</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">units</span> <span class="o">=</span> <span class="p">[</span><span class="s">'mpc'</span><span class="p">,</span><span class="s">'kpc'</span><span class="p">,</span><span class="s">'pc'</span><span class="p">,</span><span class="s">'au'</span><span class="p">]</span>
+<span class="n">my_pairs</span> <span class="o">=</span> <span class="p">[</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="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">units</span> <span class="k">for</span> <span class="n">w</span> <span class="ow">in</span> <span class="n">widths</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="s">"my_data/my_data0001"</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="n">pc</span><span class="o">.</span><span class="n">add_slice</span><span class="p">(</span><span class="n">fields</span><span class="p">[</span><span class="mf">0</span><span class="p">],</span><span class="mf">0</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="n">fields</span><span class="p">[</span><span class="mf">0</span><span class="p">],</span><span class="mf">1</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="n">fields</span><span class="p">[</span><span class="mf">0</span><span class="p">],</span><span class="mf">2</span><span class="p">)</span>
+<span class="k">for</span> <span class="n">field</span> <span class="ow">in</span> <span class="n">fields</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_pairs</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">"my_data0001_</span><span class="si">%05i%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">w</span><span class="p">,</span> <span class="n">u</span><span class="p">))</span>
+</pre></div>
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+<li><a class="reference" href="">Making Simple Plots</a><ul>
+<li><a class="reference" href="#single-width-plots">Single Width Plots</a></li>
+<li><a class="reference" href="#multiple-fields-single-width">Multiple Fields Single Width</a></li>
+<li><a class="reference" href="#single-field-multiple-widths">Single Field Multiple Widths</a></li>
+<li><a class="reference" href="#multiple-fields-multiple-widths">Multiple Fields Multiple Widths</a></li>
+</ul>
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+
+ <div class="section">
+<h1 id="making-timeseries-plots">Making Timeseries Plots<a class="headerlink" href="#making-timeseries-plots" title="Permalink to this headline">¶</a></h1>
+<p>I don’t think anyone will argue that timeseries data is important. It is
+possible to create it with yt; however, a few things should be noted.</p>
+<p>Python is notorious for leaking memory via circular references – if you
+have a variable <em>var1</em> that references variable <em>var2</em>, when one is deleted, is
+the other? Efforts have been made to identify and remove all leaking
+references, but if references are created in your code that generates the
+timeseries data, you may find that more memory is used than is desired.</p>
+<p>The process of generating time series data is fairly simple: you iterate over
+the datasets, and generate a value for each.</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">max_rho</span> <span class="o">=</span> <span class="p">[]</span>
+<span class="gp">>>> </span><span class="n">max_pos</span> <span class="o">=</span> <span class="p">[]</span>
+<span class="gp">>>> </span><span class="n">times</span> <span class="o">=</span> <span class="p">[]</span>
+<span class="gp">>>> </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">30</span><span class="p">):</span>
+<span class="gp">... </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="s">"my_output</span><span class="si">%04i</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">))</span>
+<span class="gp">... </span> <span class="n">v</span><span class="p">,</span> <span class="n">c</span> <span class="o">=</span> <span class="n">pf</span><span class="o">.</span><span class="n">h</span><span class="o">.</span><span class="n">find_max</span><span class="p">(</span><span class="s">"Density"</span><span class="p">)</span>
+<span class="gp">... </span> <span class="n">max_rho</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
+<span class="gp">... </span> <span class="n">max_pos</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+<span class="gp">... </span> <span class="n">times</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pf</span><span class="p">[</span><span class="s">"CosmologyCurrentTime"</span><span class="p">]</span> <span class="o">*</span> <span class="n">pf</span><span class="p">[</span><span class="s">"years"</span><span class="p">])</span>
+<span class="gp">>>> </span><span class="n">pylab</span><span class="o">.</span><span class="n">loglog</span><span class="p">(</span><span class="n">times</span><span class="p">,</span> <span class="n">max_rho</span><span class="p">)</span>
+<span class="gp">>>> </span><span class="n">pylab</span><span class="o">.</span><span class="n">clf</span><span class="p">()</span>
+</pre></div>
+<p>You could also imagine doing a time-evolution of an averaged quantity:</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">avg_T</span> <span class="o">=</span> <span class="p">[]</span>
+<span class="gp">>>> </span><span class="n">times</span> <span class="o">=</span> <span class="p">[]</span>
+<span class="gp">>>> </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">30</span><span class="p">):</span>
+<span class="gp">... </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="s">"my_output</span><span class="si">%04i</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">))</span>
+<span class="gp">... </span> <span class="n">v</span><span class="p">,</span> <span class="n">c</span> <span class="o">=</span> <span class="n">pf</span><span class="o">.</span><span class="n">h</span><span class="o">.</span><span class="n">find_max</span><span class="p">(</span><span class="s">"Density"</span><span class="p">)</span>
+<span class="gp">... </span> <span class="n">sp</span> <span class="o">=</span> <span class="n">pf</span><span class="o">.</span><span class="n">h</span><span class="o">.</span><span class="n">sphere</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="mf">10.0</span><span class="o">/</span><span class="n">pf</span><span class="p">[</span><span class="s">'kpc'</span><span class="p">])</span>
+<span class="gp">... </span> <span class="n">avg_T</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sp</span><span class="o">.</span><span class="n">quantities</span><span class="p">[</span><span class="s">"WeightedAverageQuantity"</span><span class="p">](</span><span class="s">"Temperature"</span><span class="p">,</span>
+<span class="gp">... </span> <span class="s">"CellMassMsun"</span><span class="p">)</span>
+<span class="gp">... </span> <span class="n">times</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pf</span><span class="p">[</span><span class="s">"CosmologyCurrentTime"</span><span class="p">]</span> <span class="o">*</span> <span class="n">pf</span><span class="p">[</span><span class="s">"years"</span><span class="p">])</span>
+<span class="gp">>>> </span><span class="n">pylab</span><span class="o">.</span><span class="n">loglog</span><span class="p">(</span><span class="n">times</span><span class="p">,</span> <span class="n">avg_T</span><span class="p">)</span>
+</pre></div>
+<p>At this point, you can also write out the data to a file and plot it in another
+plotting package:</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">"my_data.dat"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
+<span class="gp">>>> </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="nb">len</span><span class="p">(</span><span class="n">times</span><span class="p">)):</span>
+<span class="gp">... </span> <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%0.5e</span><span class="s"> </span><span class="si">%0.5e</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">times</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">avg_T</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span>
+</pre></div>
+<p>More complicated analysis can be done as well; <tt class="xref docutils literal"><span class="pre">PlotCollections</span></tt>
+created, slices made, etc.</p>
+<p>The package <tt class="xref docutils literal"><span class="pre">fido</span></tt> inside of yt is also available, but it is not
+well-documented. It will store information about outputs, associated with a
+given run, and you can iterate over those. This is altogether a simpler
+process, but it is not resilient against data movement.</p>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Next topic</h4>
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+ <h3>This Page</h3>
+ <ul class="this-page-menu">
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+ </ul>
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
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+ <li class="right"><a href="extracting_data.html" title="Extracting Data" accesskey="N">next</a> |</li>
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\ No newline at end of file
Modified: trunk/doc/build/html/extending/analyzing_in_parallel.html
==============================================================================
--- trunk/doc/build/html/extending/analyzing_in_parallel.html (original)
+++ trunk/doc/build/html/extending/analyzing_in_parallel.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Analyzing in Parallel — yt v0.3 documentation</title>
+ <title>Analyzing in Parallel — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="up" title="Extending yt" href="index.html" />
<link rel="next" title="Running Fortran Routines" href="running_fortran_routines.html" />
<link rel="prev" title="Creating Derived Fields" href="creating_derived_fields.html" />
@@ -30,9 +30,9 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="running_fortran_routines.html" title="Running Fortran Routines" accesskey="N">next</a> |</li>
<li class="right"><a href="creating_derived_fields.html" title="Creating Derived Fields" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
@@ -78,16 +78,16 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="running_fortran_routines.html" title="Running Fortran Routines" accesskey="N">next</a> |</li>
<li class="right"><a href="creating_derived_fields.html" title="Creating Derived Fields" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/extending/creating_datatypes.html
==============================================================================
--- trunk/doc/build/html/extending/creating_datatypes.html (original)
+++ trunk/doc/build/html/extending/creating_datatypes.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Creating Datatypes — yt v0.3 documentation</title>
+ <title>Creating Datatypes — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="up" title="Extending yt" href="index.html" />
<link rel="next" title="Creating Derived Quantities" href="creating_derived_quantities.html" />
<link rel="prev" title="The Plugin File" href="plugin_file.html" />
@@ -30,9 +30,9 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="creating_derived_quantities.html" title="Creating Derived Quantities" accesskey="N">next</a> |</li>
<li class="right"><a href="plugin_file.html" title="The Plugin File" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
@@ -78,16 +78,16 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="creating_derived_quantities.html" title="Creating Derived Quantities" accesskey="N">next</a> |</li>
<li class="right"><a href="plugin_file.html" title="The Plugin File" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/extending/creating_derived_fields.html
==============================================================================
--- trunk/doc/build/html/extending/creating_derived_fields.html (original)
+++ trunk/doc/build/html/extending/creating_derived_fields.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Creating Derived Fields — yt v0.3 documentation</title>
+ <title>Creating Derived Fields — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="up" title="Extending yt" href="index.html" />
<link rel="next" title="Analyzing in Parallel" href="analyzing_in_parallel.html" />
<link rel="prev" title="Creating Derived Quantities" href="creating_derived_quantities.html" />
@@ -30,9 +30,9 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="analyzing_in_parallel.html" title="Analyzing in Parallel" accesskey="N">next</a> |</li>
<li class="right"><a href="creating_derived_quantities.html" title="Creating Derived Quantities" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
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</ul>
@@ -79,16 +79,16 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="analyzing_in_parallel.html" title="Analyzing in Parallel" accesskey="N">next</a> |</li>
<li class="right"><a href="creating_derived_quantities.html" title="Creating Derived Quantities" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
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</ul>
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<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 14, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/extending/creating_derived_quantities.html
==============================================================================
--- trunk/doc/build/html/extending/creating_derived_quantities.html (original)
+++ trunk/doc/build/html/extending/creating_derived_quantities.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Creating Derived Quantities — yt v0.3 documentation</title>
+ <title>Creating Derived Quantities — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="up" title="Extending yt" href="index.html" />
<link rel="next" title="Creating Derived Fields" href="creating_derived_fields.html" />
<link rel="prev" title="Creating Datatypes" href="creating_datatypes.html" />
@@ -30,9 +30,9 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="creating_derived_fields.html" title="Creating Derived Fields" accesskey="N">next</a> |</li>
<li class="right"><a href="creating_datatypes.html" title="Creating Datatypes" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
@@ -78,16 +78,16 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="creating_derived_fields.html" title="Creating Derived Fields" accesskey="N">next</a> |</li>
<li class="right"><a href="creating_datatypes.html" title="Creating Datatypes" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
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<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Extending yt — yt v0.3 documentation</title>
+ <title>Extending yt — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="next" title="FAQ" href="../faq.html" />
<link rel="prev" title="Cookbook" href="../cookbook/index.html" />
</head>
@@ -29,9 +29,9 @@
<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="../cookbook/index.html" title="Cookbook" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -101,15 +101,15 @@
<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="../cookbook/index.html" title="Cookbook" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 14, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/extending/plugin_file.html
==============================================================================
--- trunk/doc/build/html/extending/plugin_file.html (original)
+++ trunk/doc/build/html/extending/plugin_file.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>The Plugin File — yt v0.3 documentation</title>
+ <title>The Plugin File — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="up" title="Extending yt" href="index.html" />
<link rel="next" title="Creating Datatypes" href="creating_datatypes.html" />
<link rel="prev" title="Using the Interpreter" href="using_the_interpreter.html" />
@@ -30,9 +30,9 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="creating_datatypes.html" title="Creating Datatypes" accesskey="N">next</a> |</li>
<li class="right"><a href="using_the_interpreter.html" title="Using the Interpreter" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
@@ -78,16 +78,16 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="creating_datatypes.html" title="Creating Datatypes" accesskey="N">next</a> |</li>
<li class="right"><a href="using_the_interpreter.html" title="Using the Interpreter" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/extending/running_fortran_routines.html
==============================================================================
--- trunk/doc/build/html/extending/running_fortran_routines.html (original)
+++ trunk/doc/build/html/extending/running_fortran_routines.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Running Fortran Routines — yt v0.3 documentation</title>
+ <title>Running Fortran Routines — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="up" title="Extending yt" href="index.html" />
<link rel="next" title="Extending yt" href="index.html" />
<link rel="prev" title="Analyzing in Parallel" href="analyzing_in_parallel.html" />
@@ -30,9 +30,9 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="index.html" title="Extending yt" accesskey="N">next</a> |</li>
<li class="right"><a href="analyzing_in_parallel.html" title="Analyzing in Parallel" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
@@ -78,16 +78,16 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="index.html" title="Extending yt" accesskey="N">next</a> |</li>
<li class="right"><a href="analyzing_in_parallel.html" title="Analyzing in Parallel" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/extending/using_the_interpreter.html
==============================================================================
--- trunk/doc/build/html/extending/using_the_interpreter.html (original)
+++ trunk/doc/build/html/extending/using_the_interpreter.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Using the Interpreter — yt v0.3 documentation</title>
+ <title>Using the Interpreter — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="up" title="Extending yt" href="index.html" />
<link rel="next" title="The Plugin File" href="plugin_file.html" />
<link rel="prev" title="Writing Scripts" href="writing_scripts.html" />
@@ -30,9 +30,9 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="plugin_file.html" title="The Plugin File" accesskey="N">next</a> |</li>
<li class="right"><a href="writing_scripts.html" title="Writing Scripts" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
@@ -78,16 +78,16 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="plugin_file.html" title="The Plugin File" accesskey="N">next</a> |</li>
<li class="right"><a href="writing_scripts.html" title="Writing Scripts" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/extending/writing_scripts.html
==============================================================================
--- trunk/doc/build/html/extending/writing_scripts.html (original)
+++ trunk/doc/build/html/extending/writing_scripts.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Writing Scripts — yt v0.3 documentation</title>
+ <title>Writing Scripts — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="up" title="Extending yt" href="index.html" />
<link rel="next" title="Using the Interpreter" href="using_the_interpreter.html" />
<link rel="prev" title="Extending yt" href="index.html" />
@@ -30,9 +30,9 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="using_the_interpreter.html" title="Using the Interpreter" accesskey="N">next</a> |</li>
<li class="right"><a href="index.html" title="Extending yt" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
@@ -78,16 +78,16 @@
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="using_the_interpreter.html" title="Using the Interpreter" accesskey="N">next</a> |</li>
<li class="right"><a href="index.html" title="Extending yt" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">Extending yt</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>FAQ — yt v0.3 documentation</title>
+ <title>FAQ — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
@@ -17,8 +17,8 @@
<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="yt.lagos" href="modules/lagos/index.html" />
+ <link rel="top" title="yt v0.3-pre documentation" href="index.html" />
+ <link rel="next" title="yt.lagos - Data Handling and Analysis" href="modules/lagos/index.html" />
<link rel="prev" title="Extending yt" href="extending/index.html" />
</head>
<body>
@@ -27,11 +27,11 @@
<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="modules/lagos/index.html" title="yt.lagos" accesskey="N">next</a> |</li>
+ <li class="right"><a href="modules/lagos/index.html" title="yt.lagos - Data Handling and Analysis" 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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -110,7 +110,7 @@
<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>
+first!) or attach them to a ticket at <a class="reference" href="http://yt.enzotools.org/">http://yt.enzotools.org/</a>.</p>
</div>
<div class="section">
<h2 id="how-do-i-specify-an-axis"><span id="axis-specification"></span>How do I specify an axis?<a class="headerlink" href="#how-do-i-specify-an-axis" title="Permalink to this headline">¶</a></h2>
@@ -121,7 +121,7 @@
<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>
+at the <a class="reference" href="http://yt.enzotools.org">yt homepage</a>.</p>
</div>
</div>
@@ -150,7 +150,7 @@
<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>
+ <p class="topless"><a href="modules/lagos/index.html" title="next chapter">yt.lagos - Data Handling and Analysis</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/faq.txt">Show Source</a></li>
@@ -170,17 +170,17 @@
<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="modules/lagos/index.html" title="yt.lagos - Data Handling and Analysis" 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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Index — yt v0.3 documentation</title>
+ <title>Index — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<link rel="contents" title="Global table of contents" href="contents.html" />
<link rel="index" title="Global index" href="" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="yt v0.3 documentation" href="index.html" />
+ <link rel="top" title="yt v0.3-pre documentation" href="index.html" />
</head>
<body>
<div class="related">
@@ -25,9 +25,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -50,14 +50,14 @@
<dt>2ddata</dt>
<dd><dl>
- <dt><a href="tutorial/advanced_objects.html#index-38">Cutting Plane</a></dt>
- <dt><a href="tutorial/basic_objects.html#index-50">Slices</a></dt>
+ <dt><a href="tutorial/advanced_objects.html#index-0">Cutting Plane</a></dt>
+ <dt><a href="tutorial/basic_objects.html#index-6">Slices</a></dt>
</dl></dd>
<dt>3ddata</dt>
<dd><dl>
- <dt><a href="tutorial/advanced_objects.html#index-39">Extracted Regions</a></dt>
- <dt><a href="tutorial/advanced_objects.html#index-40">GridCollection</a></dt>
- <dt><a href="tutorial/getting_started.html#index-48">grid</a></dt>
+ <dt><a href="tutorial/advanced_objects.html#index-1">Extracted Regions</a></dt>
+ <dt><a href="tutorial/advanced_objects.html#index-2">GridCollection</a></dt>
+ <dt><a href="tutorial/getting_started.html#index-9">grid</a></dt>
</dl></dd></dl></td><td width="33%" valign="top"><dl>
</dl></td></tr></table>
@@ -79,14 +79,14 @@
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.convert">(yt.lagos.Enzo3DData method)</a></dt>
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoData.convert">(yt.lagos.EnzoData method)</a></dt>
</dl></dd>
-<dt><a href="tutorial/advanced_objects.html#index-38">Cutting Plane</a></dt>
+<dt><a href="tutorial/advanced_objects.html#index-0">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-49">derivedfield</a></dt></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="tutorial/getting_started.html#index-10">derivedfield</a></dt></dl></td><td width="33%" valign="top"><dl>
</dl></td></tr></table>
<h2 id="E">E</h2>
@@ -113,7 +113,7 @@
<dt><a href="modules/lagos/outputandhierarchy.html#yt.lagos.EnzoHierarchy.export_particles_pb">export_particles_pb() (yt.lagos.EnzoHierarchy method)</a></dt>
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.extract_connected_sets">extract_connected_sets() (yt.lagos.Enzo3DData method)</a></dt>
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.extract_region">extract_region() (yt.lagos.Enzo3DData method)</a></dt>
-<dt><a href="tutorial/advanced_objects.html#index-39">Extracted Regions</a></dt>
+<dt><a href="tutorial/advanced_objects.html#index-1">Extracted Regions</a></dt>
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.ExtractedRegionBase">ExtractedRegionBase (class in yt.lagos)</a></dt>
</dl></td></tr></table>
@@ -157,8 +157,8 @@
</dl></dd></dl></td><td width="33%" valign="top"><dl>
<dt><a href="modules/lagos/outputandhierarchy.html#yt.lagos.EnzoGridBase.get_position">get_position() (yt.lagos.EnzoGridBase method)</a></dt>
<dt><a href="modules/lagos/outputandhierarchy.html#yt.lagos.EnzoHierarchy.get_smallest_dx">get_smallest_dx() (yt.lagos.EnzoHierarchy method)</a></dt>
-<dt><a href="tutorial/getting_started.html#index-48">Grid</a></dt>
-<dt><a href="tutorial/advanced_objects.html#index-40">GridCollection</a></dt>
+<dt><a href="tutorial/getting_started.html#index-9">Grid</a></dt>
+<dt><a href="tutorial/advanced_objects.html#index-2">GridCollection</a></dt>
</dl></td></tr></table>
<h2 id="H">H</h2>
@@ -177,14 +177,14 @@
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.has_key">(yt.lagos.Enzo3DData method)</a></dt>
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoData.has_key">(yt.lagos.EnzoData method)</a></dt>
</dl></dd></dl></td><td width="33%" valign="top"><dl>
-<dt><a href="tutorial/getting_started.html#index-47">hierarchy</a></dt>
+<dt><a href="tutorial/getting_started.html#index-8">hierarchy</a></dt>
</dl></td></tr></table>
<h2 id="I">I</h2>
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="tutorial/basic_objects.html#index-49">indices</a></dt>
+<dt><a href="tutorial/getting_started.html#index-10">indices</a></dt>
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData.interpolate_discretize">interpolate_discretize() (yt.lagos.Enzo2DData method)</a></dt></dl></td><td width="33%" valign="top"><dl>
</dl></td></tr></table>
@@ -193,14 +193,14 @@
<dl>
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.paint_grids">paint_grids() (yt.lagos.Enzo3DData method)</a></dt>
-<dt><a href="tutorial/automated_plotting.html#index-42">PlotCollections</a></dt>
+<dt><a href="tutorial/automated_plotting.html#index-4">PlotCollections</a></dt>
<dd><dl>
- <dt><a href="tutorial/automated_plotting.html#index-43">Adding Plots</a></dt>
+ <dt><a href="tutorial/automated_plotting.html#index-5">Adding Plots</a></dt>
</dl></dd>
-<dt><a href="tutorial/automated_plotting.html#index-41">Plotting</a></dt>
+<dt><a href="tutorial/automated_plotting.html#index-3">Plotting</a></dt>
<dd><dl>
- <dt><a href="tutorial/automated_plotting.html#index-43">Adding plots to PlotCollections</a></dt>
- <dt><a href="tutorial/automated_plotting.html#index-42">PlotCollections</a></dt>
+ <dt><a href="tutorial/automated_plotting.html#index-5">Adding plots to PlotCollections</a></dt>
+ <dt><a href="tutorial/automated_plotting.html#index-4">PlotCollections</a></dt>
</dl></dd></dl></td><td width="33%" valign="top"><dl>
<dt><a href="modules/lagos/outputandhierarchy.html#yt.lagos.EnzoHierarchy.print_stats">print_stats() (yt.lagos.EnzoHierarchy method)</a></dt>
</dl></td></tr></table>
@@ -209,7 +209,7 @@
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="tutorial/automated_plotting.html#index-42">Raven</a>, <a href="tutorial/automated_plotting.html#index-43">[Link]</a></dt>
+<dt><a href="tutorial/automated_plotting.html#index-4">Raven</a>, <a href="tutorial/automated_plotting.html#index-5">[Link]</a></dt>
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoSliceBase.reslice">reslice() (yt.lagos.EnzoSliceBase method)</a></dt></dl></td><td width="33%" valign="top"><dl>
</dl></td></tr></table>
@@ -231,8 +231,8 @@
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoData.set_field_parameter">(yt.lagos.EnzoData method)</a></dt>
</dl></dd></dl></td><td width="33%" valign="top"><dl>
<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoSliceBase.shift">shift() (yt.lagos.EnzoSliceBase method)</a></dt>
-<dt><a href="tutorial/basic_objects.html#index-50">Slices</a></dt>
-<dt><a href="tutorial/getting_started.html#index-46">Starting yt</a></dt>
+<dt><a href="tutorial/basic_objects.html#index-6">Slices</a></dt>
+<dt><a href="tutorial/getting_started.html#index-7">Starting yt</a></dt>
</dl></td></tr></table>
<h2 id="Y">Y</h2>
@@ -264,15 +264,15 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 14, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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 Overview — yt v0.3 documentation</title>
+ <title>yt Overview — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="" />
+ <link rel="top" title="yt v0.3-pre documentation" href="" />
</head>
<body>
<div class="related">
@@ -25,9 +25,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="">yt v0.3 documentation</a> »</li>
+ <li><a href="">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -59,8 +59,8 @@
<li><a class="reference" href="tutorial/profiles.html">Profiles</a></li>
<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/advanced_objects.html#derived-quantities">Derived Quantities</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>
@@ -68,6 +68,8 @@
<ul>
<li><a class="reference" href="cookbook/index.html">Cookbook</a><ul>
<li><a class="reference" href="cookbook/making_simple_plots.html">Making Simple Plots</a></li>
+<li><a class="reference" href="cookbook/making_timeseries_plots.html">Making Timeseries Plots</a></li>
+<li><a class="reference" href="cookbook/extracting_data.html">Extracting Data</a></li>
</ul>
</li>
</ul>
@@ -152,15 +154,15 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="">yt v0.3 documentation</a> »</li>
+ <li><a href="">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 14, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Introduction — yt v0.3 documentation</title>
+ <title>Introduction — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="index.html" />
<link rel="next" title="A Short Tutorial" href="tutorial/index.html" />
<link rel="prev" title="yt Overview" href="index.html" />
</head>
@@ -29,9 +29,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -164,15 +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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Global Module Index — yt v0.3 documentation</title>
+ <title>Global Module Index — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="index.html" />
</head>
<body>
<div class="related">
@@ -25,9 +25,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -75,15 +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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 14, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/modules/lagos/basedatatypes.html
==============================================================================
--- trunk/doc/build/html/modules/lagos/basedatatypes.html (original)
+++ trunk/doc/build/html/modules/lagos/basedatatypes.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Data Containers — yt v0.3 documentation</title>
+ <title>Data Containers — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../../index.html" />
<link rel="up" title="yt.lagos - Data Handling and Analysis" href="index.html" />
<link rel="prev" title="Native Enzo Data Structures" href="outputandhierarchy.html" />
</head>
@@ -28,9 +28,9 @@
<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="outputandhierarchy.html" title="Native Enzo Data Structures" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">yt.lagos - Data Handling and Analysis</a> »</li>
</ul>
@@ -153,9 +153,7 @@
<dl class="class">
<dt id="yt.lagos.Enzo2DData">
<!--#yt.lagos.Enzo2DData#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">Enzo2DData</tt><big>(</big><em>axis</em>, <em>fields</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData" title="Permalink to this definition">¶</a></dt>
-<dd><p>Class to represent a set of <a title="yt.lagos.EnzoData" class="reference" href="#yt.lagos.EnzoData"><tt class="xref docutils literal"><span class="pre">EnzoData</span></tt></a> that’s 2-D in nature, and
-thus does not have as many actions as the 3-D data types.</p>
-<p>Prepares the Enzo2DData, normal to <em>axis</em>. If <em>axis</em> is 4, we are not
+<dd><p>Prepares the Enzo2DData, normal to <em>axis</em>. If <em>axis</em> is 4, we are not
aligned with any axis.</p>
<dl class="method">
<dt id="yt.lagos.Enzo2DData.clear_data">
@@ -212,9 +210,7 @@
<dl class="class">
<dt id="yt.lagos.Enzo3DData">
<!--#yt.lagos.Enzo3DData#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">Enzo3DData</tt><big>(</big><em>center</em>, <em>fields</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData" title="Permalink to this definition">¶</a></dt>
-<dd><p>Class describing a cluster of data points, not necessarily sharing any
-particular attribute.</p>
-<p>Returns an instance of Enzo3DData, or prepares one. Usually only
+<dd><p>Returns an instance of Enzo3DData, or prepares one. Usually only
used as a base class. Note that <em>center</em> is supplied, but only used
for fields and quantities that require it.</p>
<dl class="method">
@@ -444,16 +440,16 @@
<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="outputandhierarchy.html" title="Native Enzo Data Structures" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">yt.lagos - Data Handling and Analysis</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 10, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/modules/lagos/contours.html
==============================================================================
--- trunk/doc/build/html/modules/lagos/contours.html (original)
+++ trunk/doc/build/html/modules/lagos/contours.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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 v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../../index.html" />
<link rel="up" title="yt.lagos - Data Handling and Analysis" href="index.html" />
<link rel="prev" title="Data Containers" href="basedatatypes.html" />
</head>
@@ -28,9 +28,9 @@
<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="basedatatypes.html" title="Data Containers" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">yt.lagos - Data Handling and Analysis</a> »</li>
</ul>
@@ -70,16 +70,16 @@
<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="basedatatypes.html" title="Data Containers" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">yt.lagos - Data Handling and Analysis</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 10, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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.lagos - Data Handling and Analysis — yt v0.3 documentation</title>
+ <title>yt.lagos - Data Handling and Analysis — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../../index.html" />
<link rel="prev" title="FAQ" href="../../faq.html" />
</head>
<body>
@@ -27,9 +27,9 @@
<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="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -87,15 +87,15 @@
<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="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 10, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/modules/lagos/outputandhierarchy.html
==============================================================================
--- trunk/doc/build/html/modules/lagos/outputandhierarchy.html (original)
+++ trunk/doc/build/html/modules/lagos/outputandhierarchy.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Native Enzo Data Structures — yt v0.3 documentation</title>
+ <title>Native Enzo Data Structures — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../../index.html" />
<link rel="up" title="yt.lagos - Data Handling and Analysis" href="index.html" />
<link rel="next" title="Data Containers" href="basedatatypes.html" />
<link rel="prev" title="yt.lagos - Data Handling and Analysis" href="index.html" />
@@ -30,9 +30,9 @@
<li class="right"><a href="../../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="basedatatypes.html" title="Data Containers" accesskey="N">next</a> |</li>
<li class="right"><a href="index.html" title="yt.lagos - Data Handling and Analysis" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">yt.lagos - Data Handling and Analysis</a> »</li>
</ul>
@@ -77,7 +77,7 @@
<dt id="yt.lagos.EnzoHierarchy.export_particles_pb">
<!--#yt.lagos.EnzoHierarchy.export_particles_pb#--><tt class="descname">export_particles_pb</tt><big>(</big><em>filename</em>, <em>filter=1</em>, <em>indexboundary=0</em>, <em>fields=None</em>, <em>scale=1.0</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoHierarchy.export_particles_pb" title="Permalink to this definition">¶</a></dt>
<dd>Exports all the star particles, or a subset, to pb-format <em>filename</em>
-for viewing in partiview. Filters based on particle_type=*filter*,
+for viewing in partiview. Filters based on particle_type=*filter*,
particle_index>=*indexboundary*, and exports <em>fields</em>, if supplied.
Otherwise, index, position(x,y,z). Optionally <em>scale</em> by a given
factor before outputting.</dd></dl>
@@ -142,7 +142,7 @@
<dl class="method">
<dt id="yt.lagos.EnzoHierarchy.save_data">
-<!--#yt.lagos.EnzoHierarchy.save_data#--><tt class="descname">save_data</tt><big>(</big><em>array</em>, <em>node</em>, <em>name</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoHierarchy.save_data" title="Permalink to this definition">¶</a></dt>
+<!--#yt.lagos.EnzoHierarchy.save_data#--><tt class="descname">save_data</tt><big>(</big><em>array</em>, <em>node</em>, <em>name</em>, <em>set_attr=None</em>, <em>force=False</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoHierarchy.save_data" title="Permalink to this definition">¶</a></dt>
<dd>Arbitrary numpy data will be saved to the region in the datafile
described by <em>node</em> and <em>name</em>. If data file does not exist, it throws
no error and simply does not save.</dd></dl>
@@ -245,16 +245,16 @@
<li class="right"><a href="../../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
<li class="right"><a href="basedatatypes.html" title="Data Containers" accesskey="N">next</a> |</li>
<li class="right"><a href="index.html" title="yt.lagos - Data Handling and Analysis" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">yt.lagos - Data Handling and Analysis</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 10, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/modules/lagos/profiles.html
==============================================================================
--- trunk/doc/build/html/modules/lagos/profiles.html (original)
+++ trunk/doc/build/html/modules/lagos/profiles.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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 v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../../index.html" />
<link rel="up" title="yt.lagos - Data Handling and Analysis" href="index.html" />
<link rel="next" title="yt.lagos - Data Handling and Analysis" href="index.html" />
</head>
@@ -28,9 +28,9 @@
<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 - Data Handling and Analysis" accesskey="N">next</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">yt.lagos - Data Handling and Analysis</a> »</li>
</ul>
@@ -70,16 +70,16 @@
<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 - Data Handling and Analysis" accesskey="N">next</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">yt.lagos - Data Handling and Analysis</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 10, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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 v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../../_static/jquery.js"></script>
@@ -17,8 +17,8 @@
<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="prev" title="yt.lagos" href="../lagos/index.html" />
+ <link rel="top" title="yt v0.3-pre documentation" href="../../index.html" />
+ <link rel="prev" title="yt.lagos - Data Handling and Analysis" href="../lagos/index.html" />
</head>
<body>
<div class="related">
@@ -26,10 +26,10 @@
<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 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 class="right"><a href="../lagos/index.html" title="yt.lagos - Data Handling and Analysis" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -47,7 +47,7 @@
<div class="sidebar">
<div class="sidebarwrapper">
<h4>Previous topic</h4>
- <p class="topless"><a href="../lagos/index.html" title="previous chapter">yt.lagos</a></p>
+ <p class="topless"><a href="../lagos/index.html" title="previous chapter">yt.lagos - Data Handling and Analysis</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="../../_sources/modules/raven/index.txt">Show Source</a></li>
@@ -67,16 +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="../lagos/index.html" title="yt.lagos" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li class="right"><a href="../lagos/index.html" title="yt.lagos - Data Handling and Analysis" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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 v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../../index.html" />
<link rel="next" title="yt Overview" href="../../index.html" />
</head>
<body>
@@ -27,9 +27,9 @@
<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 Overview" accesskey="N">next</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -68,15 +68,15 @@
<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="../../index.html" title="yt Overview" accesskey="N">next</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Search — yt v0.3 documentation</title>
+ <title>Search — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="" />
- <link rel="top" title="yt v0.3 documentation" href="index.html" />
+ <link rel="top" title="yt v0.3-pre documentation" href="index.html" />
<script type="text/javascript" src="_static/searchtools.js"></script>
</head>
@@ -27,9 +27,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -68,15 +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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 14, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -1 +1 @@
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\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/advanced_objects.html
==============================================================================
--- trunk/doc/build/html/tutorial/advanced_objects.html (original)
+++ trunk/doc/build/html/tutorial/advanced_objects.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Advanced Objects — yt v0.3 documentation</title>
+ <title>Advanced Objects — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
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<link rel="next" title="Projections" href="projections.html" />
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@@ -30,9 +30,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
</ul>
@@ -51,7 +51,7 @@
profile them, all of that, right from the command line like you would a sphere
or a region.</p>
<div class="section">
-<h2 id="cutting-plane"><span id="index-38"></span>Cutting Plane<a class="headerlink" href="#cutting-plane" title="Permalink to this headline">¶</a></h2>
+<h2 id="cutting-plane"><span id="index-0"></span>Cutting Plane<a class="headerlink" href="#cutting-plane" title="Permalink to this headline">¶</a></h2>
<p>The first of these is the cutting plane. Let’s say you’re doing some
collapse-based problem, where you end up with a vector that describes the
angular momentum. By feeding this vector into the cutting plane object, you can
@@ -70,7 +70,7 @@
and then used to define the transformed coordinate system.</p>
</div>
<div class="section">
-<h2 id="extracted-regions"><span id="index-39"></span>Extracted Regions<a class="headerlink" href="#extracted-regions" title="Permalink to this headline">¶</a></h2>
+<h2 id="extracted-regions"><span id="index-1"></span>Extracted Regions<a class="headerlink" href="#extracted-regions" title="Permalink to this headline">¶</a></h2>
<p>One of the other interesting data types is mostly only useful for profiles in
one and two dimensions. By whatever criteria you like, you can extract a subset
of any 3D data object. What this means is that you can apply ‘cuts’ to the data –
@@ -95,8 +95,31 @@
method, and that’s the functionality we use here.</p>
</div>
<div class="section">
-<h2 id="grid-collections"><span id="index-40"></span>Grid Collections<a class="headerlink" href="#grid-collections" title="Permalink to this headline">¶</a></h2>
+<h2 id="grid-collections"><span id="index-2"></span>Grid Collections<a class="headerlink" href="#grid-collections" title="Permalink to this headline">¶</a></h2>
</div>
+<div class="section">
+<h2 id="disks">Disks<a class="headerlink" href="#disks" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section">
+<h2 id="clumps">Clumps<a class="headerlink" href="#clumps" title="Permalink to this headline">¶</a></h2>
+</div>
+</div>
+<div class="section">
+<h1 id="derived-quantities">Derived Quantities<a class="headerlink" href="#derived-quantities" title="Permalink to this headline">¶</a></h1>
+<p>Associated with a given data object, one can imagine various quantities being
+described. Several of these are already included in yt, and more can be added.
+To access a derived quantity, the property ‘quantities’ is available in a given
+data object. It acts as a dictionary, returning callable functions.:</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">L_vec</span> <span class="o">=</span> <span class="n">gal1_region</span><span class="o">.</span><span class="n">quantities</span><span class="p">[</span><span class="s">"AngularMomentumVector"</span><span class="p">]()</span>
+<span class="gp">>>> </span><span class="n">com</span> <span class="o">=</span> <span class="n">gal1_region</span><span class="o">.</span><span class="n">quantities</span><span class="p">[</span><span class="s">"CenterOfMass"</span><span class="p">]()</span>
+<span class="gp">>>> </span><span class="n">avg_T</span> <span class="o">=</span> <span class="n">gal1_region</span><span class="o">.</span><span class="n">quantities</span><span class="p">[</span><span class="s">"WeightedAverageQuantity"</span><span class="p">](</span><span class="s">"Temperature"</span><span class="p">,</span> \
+<span class="gp">... </span> <span class="s">"CellMassMsun"</span><span class="p">)</span>
+</pre></div>
+<p>All derived quantities accept the parameter <tt class="xref docutils literal"><span class="pre">lazy_reader</span></tt>, which
+tells the function to attempt to operate in a memory-conservative fashion –
+reading and then flushing the data back to disk. This is not possible for all
+functions, notably the <tt class="xref docutils literal"><span class="pre">IsBound()</span></tt> function, which checks for
+gravitationally-bound status.</p>
</div>
@@ -111,8 +134,11 @@
<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>
+<li><a class="reference" href="#disks">Disks</a></li>
+<li><a class="reference" href="#clumps">Clumps</a></li>
</ul>
</li>
+<li><a class="reference" href="#derived-quantities">Derived Quantities</a></li>
</ul>
<h4>Previous topic</h4>
@@ -140,16 +166,16 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre 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 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Automated Plotting — yt v0.3 documentation</title>
+ <title>Automated Plotting — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.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" />
@@ -30,9 +30,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
</ul>
@@ -44,12 +44,12 @@
<div class="section">
-<h1 id="automated-plotting"><span id="index-41"></span>Automated Plotting<a class="headerlink" href="#automated-plotting" title="Permalink to this headline">¶</a></h1>
+<h1 id="automated-plotting"><span id="index-3"></span>Automated Plotting<a class="headerlink" href="#automated-plotting" title="Permalink to this headline">¶</a></h1>
<p>So now we know how to get and manipulate most of the datatypes, but we
still have to go through some processes to plot them manually. However, yt has
facilities for plotting slices, projections and profiles in much easier ways.</p>
<div class="section">
-<h2 id="collections-of-plots"><span id="index-42"></span>Collections of Plots<a class="headerlink" href="#collections-of-plots" title="Permalink to this headline">¶</a></h2>
+<h2 id="collections-of-plots"><span id="index-4"></span>Collections of Plots<a class="headerlink" href="#collections-of-plots" title="Permalink to this headline">¶</a></h2>
<p>The plotting tool is called ‘raven’ and it’s organized around the idea of
PlotCollection objects. Each PlotCollection object is in some way thematically
associated – maybe they are all the same data, sliced along different axes, for instance.
@@ -60,7 +60,7 @@
</pre></div>
</div>
<div class="section">
-<h2 id="adding-plots"><span id="index-43"></span>Adding Plots<a class="headerlink" href="#adding-plots" title="Permalink to this headline">¶</a></h2>
+<h2 id="adding-plots"><span id="index-5"></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>
@@ -88,7 +88,7 @@
<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>
+<span class="gp">>>> </span><span class="n">pc</span><span class="o">.</span><span class="n">add_phase_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>
@@ -134,16 +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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre 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 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Basic Objects — yt v0.3 documentation</title>
+ <title>Basic Objects — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.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" />
@@ -30,9 +30,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
</ul>
@@ -45,13 +45,8 @@
<div class="section">
<h1 id="id1"><span id="basic-objects"></span>Basic Objects<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h1>
-<p>What the code just did was access the grid files and then spit back the
-results of the read operations. So we can access the fields pretty easily
-this way, but what about generating new fields from our existing fields?
-Well, that’s just as easy! And yt comes with many derived fields
-pre-defined, but from within a script you can also define your own.</p>
<div class="section">
-<h2 id="derived-fields-and-indices"><span id="index-49"></span>Derived Fields and Indices<a class="headerlink" href="#derived-fields-and-indices" title="Permalink to this headline">¶</a></h2>
+<h2 id="derived-fields-and-indices">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>
@@ -66,6 +61,9 @@
<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">"Density"</span><span class="p">][</span><span class="mf">0</span><span class="p">,:,</span><span class="mf">4</span><span class="p">]</span>
<span class="gp">>>> </span><span class="k">print</span> <span class="n">my_grid</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="mf">2</span><span class="p">:</span><span class="mf">4</span><span class="p">,</span><span class="mf">4</span><span class="p">]</span>
</pre></div>
+<p>The first will return to us everything where the x index is zero and the z
+index is four. The second will return the same, except restrict the return to
+only between indices 2 and 4.</p>
<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
@@ -74,7 +72,7 @@
fixed-resolution grids and cutting planes from the herarchy.</p>
</div>
<div class="section">
-<h2 id="slices"><span id="index-50"></span>Slices<a class="headerlink" href="#slices" title="Permalink to this headline">¶</a></h2>
+<h2 id="slices"><span id="index-6"></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>
@@ -92,12 +90,17 @@
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>
+<h2 id="boxes">Boxes<a class="headerlink" href="#boxes" 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>
+<p>This data object will respect a fixed protocol, as will all the 3D objects.
+You ask it for a field, and it returns that field:</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">my_region</span><span class="p">[</span><span class="s">"Density"</span><span class="p">]</span>
+</pre></div>
+<p>We’ll talk more about which fields are available in the next section.</p>
</div>
</div>
@@ -112,7 +115,7 @@
<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>
+<li><a class="reference" href="#boxes">Boxes</a></li>
</ul>
</li>
</ul>
@@ -142,16 +145,16 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre 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 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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 Fields — yt v0.3 documentation</title>
+ <title>Derived Fields — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.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" />
@@ -30,9 +30,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
</ul>
@@ -59,7 +59,7 @@
</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,
+<p>There are <strong>lots</strong>. 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>
<div class="highlight"><pre><span class="gp">>>> </span><span class="k">def</span> <span class="nf">_DensityCubed</span><span class="p">(</span><span class="n">field</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span>
@@ -135,16 +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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre 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 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/example_script.html
==============================================================================
--- trunk/doc/build/html/tutorial/example_script.html (original)
+++ trunk/doc/build/html/tutorial/example_script.html Mon Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>
+ <title>A Demonstrative Example Script — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,10 +17,10 @@
<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="top" title="yt v0.3-pre 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" />
+ <link rel="prev" title="Projections" href="projections.html" />
</head>
<body>
<div class="related">
@@ -29,10 +29,10 @@
<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="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 class="right"><a href="projections.html" title="Projections" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
</ul>
@@ -85,7 +85,7 @@
<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>
+ <p class="topless"><a href="projections.html" title="previous chapter">Projections</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>
@@ -108,17 +108,17 @@
<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 class="right"><a href="projections.html" title="Projections" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre 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 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Getting Started — yt v0.3 documentation</title>
+ <title>Getting Started — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="up" title="A Short Tutorial" href="index.html" />
<link rel="next" title="Basic Objects" href="basic_objects.html" />
<link rel="prev" title="A Short Tutorial" href="index.html" />
@@ -30,9 +30,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
</ul>
@@ -46,7 +46,7 @@
<div class="section">
<h1 id="getting-started">Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
<div class="section">
-<h2 id="getting-into-yt"><span id="index-46"></span>Getting into yt<a class="headerlink" href="#getting-into-yt" title="Permalink to this headline">¶</a></h2>
+<h2 id="getting-into-yt"><span id="index-7"></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>
@@ -60,30 +60,43 @@
friend.</p>
<div class="highlight"><pre><span class="gp">>>> </span><span class="k">import</span> <span class="nn">yt.lagos</span> <span class="k">as</span> <span class="nn">lagos</span>
</pre></div>
+<p>The <a title="The data handling done with Enzo data" class="reference" href="../modules/lagos/index.html"><tt class="xref docutils literal"><span class="pre">yt.lagos</span></tt></a> module is now in our namespace and called <tt class="xref docutils literal"><span class="pre">lagos</span></tt>; you
+can import it as whatever you like, but we’ll stick with that for the remainder
+of the tutorial. Let’s move on to opening an output.</p>
</div>
<div class="section">
-<h2 id="the-hierarchy"><span id="index-47"></span>The Hierarchy<a class="headerlink" href="#the-hierarchy" title="Permalink to this headline">¶</a></h2>
-<p>We first instantiate a StaticOutput. This is a pretty simple process - lagos
+<h2 id="the-hierarchy"><span id="index-8"></span>The Hierarchy<a class="headerlink" href="#the-hierarchy" title="Permalink to this headline">¶</a></h2>
+<p>We first instantiate a StaticOutput, which is a single disk-written timestep of
+the simulation This is a pretty simple process - <tt class="xref docutils literal"><span class="pre">lagos</span></tt>
will grab the parameter file that you give it, parse it, set up some handy
units, and then return control to you.:</p>
-<div class="highlight"><pre><span class="gp">>>> </span><span class="n">a</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="s">"/Users/matthewturk/Research/data/DataDir0036/DataDump0036"</span><span class="p">)</span>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">a</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="s">"my_data0001.dir/my_data0001"</span><span class="p">)</span>
</pre></div>
<p>But what good is just a parameter file? What we really want is to be able to
manipulate the grids, and all the fields stored in those grids. Fortunately,
-we can access the hierarchy as either ‘hierarchy’ or ‘h’.
-Let’s start out by finding the location of the maximum Density.
+we can access the hierarchy as either ‘hierarchy’ or ‘h’.</p>
+<p>The ‘h’ property will instantiate an <tt class="xref docutils literal"><span class="pre">EnzoHierarchy</span></tt> object, which
+posseses information about the grids in a given output, as well as their
+spatial relationships to each other. Furthermore, <tt class="xref docutils literal"><span class="pre">yt</span></tt> will store
+commonly-used and expensive-to-generate data in an HDF5 file associated with
+that object – things like projections, 3D phase profiles, and so on.</p>
+<p>All of the data-handling we want to do will be mediated by the hierarchy file;
+so let’s start out by finding the location of the maximum Density.
Note that here we use an inline-unpacking – find_max returns two values,
packed into a tuple, so we manually unpack them right here.:</p>
<div class="highlight"><pre><span class="gp">>>> </span><span class="n">v</span><span class="p">,</span><span class="n">c</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">find_max</span><span class="p">(</span><span class="s">"Density"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="k">print</span> <span class="n">v</span>
<span class="gp">>>> </span><span class="k">print</span> <span class="n">c</span>
</pre></div>
+<p id="index-9">Now we know where the maximum density is located, and what it is. This is a
+pretty simple process, and we will use it later to center spheres and boxes and
+disks on the point of maximum density.</p>
</div>
<div class="section">
-<h2 id="the-grids"><span id="index-48"></span>The Grids<a class="headerlink" href="#the-grids" title="Permalink to this headline">¶</a></h2>
+<h2 id="the-grids">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>
+<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 first grid in the hierarchy</span>
<span class="gp">>>> </span><span class="k">print</span> <span class="n">my_grid</span><span class="o">.</span><span class="n">dx</span><span class="p">,</span> <span class="n">my_grid</span><span class="o">.</span><span class="n">ActiveDimensions</span> <span class="c"># Some of the attributes</span>
</pre></div>
<p>You might be asking yourself, how do I know what properties objects have?
@@ -97,7 +110,14 @@
object.</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">"Density"</span><span class="p">]</span><span class="o">*</span><span class="n">my_grid</span><span class="p">[</span><span class="s">"Temperature"</span><span class="p">]</span>
</pre></div>
-</div>
+<p>What the code just did was access the grid files and then spit back the
+results of the read operations. So we can access the fields pretty easily
+this way, but what about generating new fields from our existing fields?
+Well, that’s just as easy! And yt comes with many derived fields
+pre-defined, but from within a script you can also define your own. In the
+next section we’ll take about the difference between a native field and a
+derived field.</p>
+<span class="target" id="index-10"></span></div>
</div>
@@ -141,16 +161,16 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre 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 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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 Short Tutorial — yt v0.3 documentation</title>
+ <title>A Short Tutorial — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,8 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
+ <link rel="next" title="Cookbook" href="../cookbook/index.html" />
<link rel="prev" title="Introduction" href="../intro.html" />
</head>
<body>
@@ -26,10 +27,11 @@
<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="../cookbook/index.html" title="Cookbook" accesskey="N">next</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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
@@ -58,7 +60,7 @@
<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>
+<li><a class="reference" href="basic_objects.html#boxes">Boxes</a></li>
</ul>
</li>
</ul>
@@ -73,6 +75,7 @@
<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>
+<li><a class="reference" href="profiles.html#three-dimensional-profiles">Three-Dimensional Profiles</a></li>
</ul>
</li>
</ul>
@@ -89,8 +92,11 @@
<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>
+<li><a class="reference" href="advanced_objects.html#disks">Disks</a></li>
+<li><a class="reference" href="advanced_objects.html#clumps">Clumps</a></li>
</ul>
</li>
+<li><a class="reference" href="advanced_objects.html#derived-quantities">Derived Quantities</a></li>
</ul>
<ul>
<li><a class="reference" href="projections.html">Projections</a><ul>
@@ -100,9 +106,6 @@
</li>
</ul>
<ul>
-<li><a class="reference" href="derived_quantities.html">Derived Quantities</a></li>
-</ul>
-<ul>
<li><a class="reference" href="example_script.html">A Demonstrative Example Script</a></li>
</ul>
</div>
@@ -115,6 +118,8 @@
<div class="sidebarwrapper">
<h4>Previous topic</h4>
<p class="topless"><a href="../intro.html" title="previous chapter">Introduction</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="../cookbook/index.html" title="next chapter">Cookbook</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="../_sources/tutorial/index.txt">Show Source</a></li>
@@ -134,16 +139,17 @@
<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="../cookbook/index.html" title="Cookbook" accesskey="N">next</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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2008, Matthew Turk.
- Last updated on May 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Profiles — yt v0.3 documentation</title>
+ <title>Profiles — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,7 +17,7 @@
<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="top" title="yt v0.3-pre documentation" href="../index.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" />
@@ -30,9 +30,9 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
</ul>
@@ -46,7 +46,7 @@
<div class="section">
<h1 id="profiles">Profiles<a class="headerlink" href="#profiles" title="Permalink to this headline">¶</a></h1>
<p>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,
+of one or more variables, along one, two or three different dimensions. For example,
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>
@@ -83,6 +83,8 @@
<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>
+<p>Note that we manually plot it, but <tt class="xref docutils literal"><span class="pre">raven</span></tt> also includes an automated
+plotting method for obtaining and displaying radial profiles.</p>
</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>
@@ -94,6 +96,52 @@
<span class="gp">>>> </span><span class="n">pylab</span><span class="o">.</span><span class="n">pcolormesh</span><span class="p">(</span><span class="n">prof2d</span><span class="p">[</span><span class="s">"Density"</span><span class="p">],</span> <span class="n">prof2d</span><span class="p">[</span><span class="s">"Temperature"</span><span class="p">],</span>
<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>
+<p>Again, we have manually plotted this, but an automated plotter is available.:</p>
+<div class="highlight"><pre><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_phase_object</span><span class="p">(</span><span class="n">sphere</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">"x-velocity"</span><span class="p">],</span>
+<span class="gp">... </span> <span class="mf">16</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</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="gp">... </span> <span class="mf">16</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span> <span class="p">(</span><span class="mf">1e2</span><span class="p">,</span> <span class="mf">1e5</span><span class="p">),</span> <span class="n">lazy_reader</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+</pre></div>
+<p>The API is slightly different here, but it will accept any object (a sphere in
+our case) and generate the profile based on the arguments. If you simply want
+a sphere, you can ask for that and the sphere will be generated as well – and
+the function will automatically generate the bounds. (Although, keep in mind,
+if you do not supply bounds it will have to read the data into memory, which
+means you are no longer able to use the <tt class="xref docutils literal"><span class="pre">lazy_reader</span></tt> functionality.
+This will change in future versions.)</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">pc</span><span class="o">.</span><span class="n">add_phase_sphere</span><span class="p">(</span><span class="mf">0.1</span><span class="p">,</span> <span class="s">'kpc'</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">"x-velocity"</span><span class="p">])</span>
+</pre></div>
+</div>
+<div class="section">
+<h2 id="three-dimensional-profiles">Three-Dimensional Profiles<a class="headerlink" href="#three-dimensional-profiles" title="Permalink to this headline">¶</a></h2>
+<img align="left" alt="../_images/example_3dphase.png" class="align-left" src="../_images/example_3dphase.png" style="width: 250px;" />
+<p>If you have the <a class="reference" href="http://astronomy.swin.edu.au/s2plot/index.php?title=S2PLOT">S2PLOT</a>
+bindings installed, you can visualize three-dimensional profiles with yt. The
+API is nearly identical to that used to generate the lower-dimensionality
+profiles.</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">prof</span> <span class="o">=</span> <span class="n">lagos</span><span class="o">.</span><span class="n">BinnedProfile3D</span><span class="p">(</span><span class="n">sphere</span><span class="p">,</span>
+<span class="gp">... </span> <span class="mf">128</span><span class="p">,</span> <span class="s">"Density"</span><span class="p">,</span> <span class="n">extrema</span><span class="p">[</span><span class="mf">0</span><span class="p">][</span><span class="mf">0</span><span class="p">],</span> <span class="n">extrema</span><span class="p">[</span><span class="mf">0</span><span class="p">][</span><span class="mf">1</span><span class="p">],</span> <span class="bp">True</span><span class="p">,</span>
+<span class="gp">... </span> <span class="mf">128</span><span class="p">,</span> <span class="s">"Temperature"</span><span class="p">,</span> <span class="n">extrema</span><span class="p">[</span><span class="mf">1</span><span class="p">][</span><span class="mf">0</span><span class="p">],</span> <span class="n">extrema</span><span class="p">[</span><span class="mf">1</span><span class="p">][</span><span class="mf">1</span><span class="p">],</span> <span class="bp">True</span><span class="p">,</span>
+<span class="gp">... </span> <span class="mf">128</span><span class="p">,</span> <span class="s">"z-velocity"</span><span class="p">,</span> <span class="n">extrema</span><span class="p">[</span><span class="mf">2</span><span class="p">][</span><span class="mf">0</span><span class="p">],</span> <span class="n">extrema</span><span class="p">[</span><span class="mf">2</span><span class="p">][</span><span class="mf">1</span><span class="p">],</span> <span class="bp">True</span><span class="p">,</span>
+<span class="gp">... </span> <span class="n">lazy_reader</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+<span class="gp">>>> </span><span class="n">prof</span><span class="o">.</span><span class="n">add_fields</span><span class="p">(</span><span class="s">"CellMassMsun"</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
+</pre></div>
+<p>I’ve wrapped the bounds into the variable <em>extrema</em>, to make it more clear.
+Once you have this profile, you can plot it with S2PLOT by calling initializing
+a 3D plot and calling <tt class="xref docutils literal"><span class="pre">run()</span></tt>.</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">vrc</span> <span class="o">=</span> <span class="n">raven</span><span class="o">.</span><span class="n">VolumeRendering3DProfile</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="s">"CellMassMsun"</span><span class="p">,</span> <span class="n">amax</span><span class="o">=</span><span class="mf">1.0</span><span class="p">)</span>
+<span class="gp">>>> </span><span class="n">vrc</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
+</pre></div>
+<p>They can be generated anywhere – and serialized – so if you want to generate
+them on a remote machine and use a local-machine for display, you only have to
+call <tt class="xref docutils literal"><span class="pre">store()</span></tt> and then initialize, instead of the standard
+<tt class="xref docutils literal"><span class="pre">BinnedProfile3D</span></tt>, <tt class="xref docutils literal"><span class="pre">StoredBinnedProfile3D</span></tt>.</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="n">prof</span><span class="o">.</span><span class="n">store_profile</span><span class="p">(</span><span class="s">'MyProfile'</span><span class="p">)</span>
+<span class="gp">>>> </span><span class="n">new_prof</span> <span class="o">=</span> <span class="n">lagos</span><span class="o">.</span><span class="n">StoredBinnedProfile3D</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="s">'MyProfile'</span><span class="p">)</span>
+</pre></div>
+<p>The retrieved profile is static, and new data cannot be added. However, it
+becomes useful in the likely circumstance that your data is stored on a machine
+on which is inconvenient to do OpenGL-based data exploration.</p>
</div>
</div>
@@ -108,6 +156,7 @@
<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>
+<li><a class="reference" href="#three-dimensional-profiles">Three-Dimensional Profiles</a></li>
</ul>
</li>
</ul>
@@ -137,16 +186,16 @@
<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="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre 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 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 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 Jun 16 12:45:22 2008
@@ -2,13 +2,13 @@
"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>Projections — yt v0.3 documentation</title>
+ <title>Projections — yt v0.3-pre 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'
+ VERSION: '0.3-pre'
};
</script>
<script type="text/javascript" src="../_static/jquery.js"></script>
@@ -17,9 +17,9 @@
<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="top" title="yt v0.3-pre documentation" href="../index.html" />
<link rel="up" title="A Short Tutorial" href="index.html" />
- <link rel="next" title="Derived Quantities" href="derived_quantities.html" />
+ <link rel="next" title="A Demonstrative Example Script" href="example_script.html" />
<link rel="prev" title="Advanced Objects" href="advanced_objects.html" />
</head>
<body>
@@ -28,11 +28,11 @@
<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="derived_quantities.html" title="Derived Quantities" accesskey="N">next</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="advanced_objects.html" title="Advanced Objects" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre documentation</a> »</li>
<li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
</ul>
@@ -91,7 +91,7 @@
<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="derived_quantities.html" title="next chapter">Derived Quantities</a></p>
+ <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/projections.txt">Show Source</a></li>
@@ -111,18 +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="derived_quantities.html" title="Derived Quantities" accesskey="N">next</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="advanced_objects.html" title="Advanced Objects" accesskey="P">previous</a> |</li>
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
- <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+ <li><a href="../index.html">yt v0.3-pre 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 09, 2008.
+ © Copyright 2008, Matthew J. Turk.
+ Last updated on Jun 16, 2008.
</div>
</body>
</html>
\ No newline at end of file
Added: trunk/doc/source/.static/override.css
==============================================================================
--- (empty file)
+++ trunk/doc/source/.static/override.css Mon Jun 16 12:45:22 2008
@@ -0,0 +1,3 @@
+.documentwrapper {
+ background: #000000;
+}
Modified: trunk/doc/source/.templates/layout.html
==============================================================================
--- trunk/doc/source/.templates/layout.html (original)
+++ trunk/doc/source/.templates/layout.html Mon Jun 16 12:45:22 2008
@@ -1,5 +1,5 @@
{% extends "!layout.html" %}
{% block rootrellink %}
- <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+ <li><a href="http://yt.enzotools.org/">yt</a> »</li>
{{ super() }}
{% endblock %}
Added: trunk/doc/source/_images/example_3dphase.png
==============================================================================
Binary file. No diff available.
Added: trunk/doc/source/_images/example_cuttingplane.png
==============================================================================
Binary file. No diff available.
Added: trunk/doc/source/_images/example_phaseplot.png
==============================================================================
Binary file. No diff available.
Modified: trunk/doc/source/conf.py
==============================================================================
--- trunk/doc/source/conf.py (original)
+++ trunk/doc/source/conf.py Mon Jun 16 12:45:22 2008
@@ -39,7 +39,7 @@
# General substitutions.
project = 'yt'
-copyright = '2008, Matthew Turk'
+copyright = '2008, Matthew J. Turk'
# The default replacements for |version| and |release|, also used in various
# other places throughout the built documents.
@@ -47,7 +47,7 @@
# The short X.Y version.
version = '0.3'
# The full version, including alpha/beta/rc tags.
-release = '0.3'
+release = '0.3-pre'
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
Added: trunk/doc/source/cookbook/analyzing_data.rst
==============================================================================
Added: trunk/doc/source/cookbook/extracting_data.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/cookbook/extracting_data.rst Mon Jun 16 12:45:22 2008
@@ -0,0 +1,26 @@
+Extracting Data
+===============
+
+Oftentimes you will want to export data from yt to plot in another plotting
+package, or to compare against another set of data elsewhere. (Although, note
+should be made that ever effort has been made to make yt into a
+publication-quality plotter.)
+
+Data objects all have the :meth:`write_out` method, which accepts a field
+list and a filename. This will dump to text.
+
+However, if you have `PyTables <http://www.pytables.org/>`_ installed, you can
+also export things in a different way: ::
+
+ >>> cube = pf.h.smoothed_covering_grid(3, left_edge=[0.0,0.0,0.0],
+ ... right_edge=[1.0,1.0,1.0],
+ ... dims=[512,512,512],
+ ... fields=["Density"])
+ >>> f = tables.openFile("my_cube.h5","w")
+ >>> f.createArray("/","my_cube_density", cube["Density"])
+ >>> f.close()
+
+This will generate an HDF5 file with the "Density" array from our smoothed cube
+at the root node, and called "my_cube_density". With PyTables you can nest
+these, set attributes, and access the data through any application that can
+read HDF5.
Added: trunk/doc/source/cookbook/grouping_data.rst
==============================================================================
Added: trunk/doc/source/cookbook/making_movies.rst
==============================================================================
Added: trunk/doc/source/cookbook/making_simple_plots.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/cookbook/making_simple_plots.rst Mon Jun 16 12:45:22 2008
@@ -0,0 +1,91 @@
+Making Simple Plots
+===================
+
+Single Width Plots
+------------------
+
+Making plots can be considered one of the simplest things to do in yt, and at
+its most primitive you can simply declare which plots to make.
+
+The following recipe opens the parameter file, creates a 'collection' of plots,
+adds a few slices, and then saves it at a fixed width.
+
+.. code-block:: python
+
+ pf = lagos.EnzoStaticOutput("my_data/my_data0001")
+ pc = raven.PlotCollection(pf)
+ pc.add_slice("Density",0)
+ pc.add_slice("Density",1)
+ pc.add_slice("Density",2)
+ pc.set_width(100.0,'kpc')
+ pc.save("my_data0001_100kpc")
+
+Multiple Fields Single Width
+----------------------------
+
+The 'save' command encodes the name of the field into the filename. It is more
+efficient to 'switch' a field than to add a new slice with a different field.
+
+.. code-block:: python
+
+ fields = ["Density", "Temperature", "x-velocity"]
+ pf = lagos.EnzoStaticOutput("my_data/my_data0001")
+ pc = raven.PlotCollection(pf)
+ pc.add_slice(fields[0],0)
+ pc.add_slice(fields[0],1)
+ pc.add_slice(fields[0],2)
+ pc.set_width(100.0,'kpc')
+ for field in fields:
+ pc.switch_field(field)
+ pc.save("my_data0001_100kpc")
+
+Single Field Multiple Widths
+----------------------------
+
+We can zoom in on our slice very easily, and we can define it to do that and
+vary units, too, thus ensuring we have a consistent set of plots.
+
+.. note::
+ We do some fancy footwork here with the creation of *my_pairs* but it is an
+ idiom that can be applied elsewhere.
+
+.. code-block:: python
+
+ widths = [1000.0, 100.0, 10.0, 1.0]
+ units = ['mpc','kpc','pc','au']
+ my_pairs = [ (w,u) for u in units for w in widths ]
+
+ pf = lagos.EnzoStaticOutput("my_data/my_data0001")
+ pc = raven.PlotCollection(pf)
+ pc.add_slice("Density",0)
+ pc.add_slice("Density",1)
+ pc.add_slice("Density",2)
+ for w, u in my_pairs:
+ pc.set_width(w,u)
+ pc.save("my_data0001_%05i%s" % (w, u))
+
+Multiple Fields Multiple Widths
+-------------------------------
+
+Because of the way the slices are created and the fields handled, we set our
+outer loop to be over the field and the inner loop to be over the widths.
+
+.. code-block:: python
+
+ fields = ["Density", "Temperature", "x-velocity"]
+ widths = [1000.0, 100.0, 10.0, 1.0]
+ units = ['mpc','kpc','pc','au']
+ my_pairs = [ (w,u) for u in units for w in widths ]
+
+ pf = lagos.EnzoStaticOutput("my_data/my_data0001")
+ pc = raven.PlotCollection(pf)
+ pc.add_slice(fields[0],0)
+ pc.add_slice(fields[0],1)
+ pc.add_slice(fields[0],2)
+ for field in fields:
+ pc.switch_field(field)
+ for w, u in my_pairs:
+ pc.set_width(w,u)
+ pc.save("my_data0001_%05i%s" % (w, u))
+
+
Added: trunk/doc/source/cookbook/making_timeseries_plots.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/cookbook/making_timeseries_plots.rst Mon Jun 16 12:45:22 2008
@@ -0,0 +1,54 @@
+Making Timeseries Plots
+=======================
+
+I don't think anyone will argue that timeseries data is important. It is
+possible to create it with yt; however, a few things should be noted.
+
+Python is notorious for leaking memory via circular references -- if you
+have a variable *var1* that references variable *var2*, when one is deleted, is
+the other? Efforts have been made to identify and remove all leaking
+references, but if references are created in your code that generates the
+timeseries data, you may find that more memory is used than is desired.
+
+The process of generating time series data is fairly simple: you iterate over
+the datasets, and generate a value for each. ::
+
+ >>> max_rho = []
+ >>> max_pos = []
+ >>> times = []
+ >>> for i in range(30):
+ ... pf = lagos.EnzoStaticOutput("my_output%04i" % (i))
+ ... v, c = pf.h.find_max("Density")
+ ... max_rho.append(v)
+ ... max_pos.append(c)
+ ... times.append(pf["CosmologyCurrentTime"] * pf["years"])
+ >>> pylab.loglog(times, max_rho)
+ >>> pylab.clf()
+
+You could also imagine doing a time-evolution of an averaged quantity::
+
+ >>> avg_T = []
+ >>> times = []
+ >>> for i in range(30):
+ ... pf = lagos.EnzoStaticOutput("my_output%04i" % (i))
+ ... v, c = pf.h.find_max("Density")
+ ... sp = pf.h.sphere(c, 10.0/pf['kpc'])
+ ... avg_T.append(sp.quantities["WeightedAverageQuantity"]("Temperature",
+ ... "CellMassMsun")
+ ... times.append(pf["CosmologyCurrentTime"] * pf["years"])
+ >>> pylab.loglog(times, avg_T)
+
+At this point, you can also write out the data to a file and plot it in another
+plotting package: ::
+
+ >>> f = open("my_data.dat", "w")
+ >>> for i in range(len(times)):
+ ... f.write("%0.5e %0.5e\n" % (times[i], avg_T[i]))
+
+More complicated analysis can be done as well; :class:`PlotCollections`
+created, slices made, etc.
+
+The package :mod:`fido` inside of yt is also available, but it is not
+well-documented. It will store information about outputs, associated with a
+given run, and you can iterate over those. This is altogether a simpler
+process, but it is not resilient against data movement.
Modified: trunk/doc/source/faq.rst
==============================================================================
--- trunk/doc/source/faq.rst (original)
+++ trunk/doc/source/faq.rst Mon Jun 16 12:45:22 2008
@@ -80,7 +80,7 @@
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/>`_.
+first!) or attach them to a ticket at `<http://yt.enzotools.org/>`_.
.. _axis-specification:
@@ -95,4 +95,4 @@
---------------------------
I've set up a ``yt-users`` mailing list. There's more information about it
-at the `yt homepage <http://yt.spacepope.org>`_.
+at the `yt homepage <http://yt.enzotools.org>`_.
Added: trunk/doc/source/static/default.css
==============================================================================
Modified: trunk/doc/source/tutorial/advanced_objects.rst
==============================================================================
--- trunk/doc/source/tutorial/advanced_objects.rst (original)
+++ trunk/doc/source/tutorial/advanced_objects.rst Mon Jun 16 12:45:22 2008
@@ -64,3 +64,29 @@
Grid Collections
----------------
+
+Disks
+-----
+
+Clumps
+------
+
+Derived Quantities
+==================
+
+Associated with a given data object, one can imagine various quantities being
+described. Several of these are already included in yt, and more can be added.
+To access a derived quantity, the property 'quantities' is available in a given
+data object. It acts as a dictionary, returning callable functions.::
+
+ >>> L_vec = gal1_region.quantities["AngularMomentumVector"]()
+ >>> com = gal1_region.quantities["CenterOfMass"]()
+ >>> avg_T = gal1_region.quantities["WeightedAverageQuantity"]("Temperature", \
+ ... "CellMassMsun")
+
+All derived quantities accept the parameter :keyword:`lazy_reader`, which
+tells the function to attempt to operate in a memory-conservative fashion --
+reading and then flushing the data back to disk. This is not possible for all
+functions, notably the :func:`IsBound` function, which checks for
+gravitationally-bound status.
+
Modified: trunk/doc/source/tutorial/automated_plotting.rst
==============================================================================
--- trunk/doc/source/tutorial/automated_plotting.rst (original)
+++ trunk/doc/source/tutorial/automated_plotting.rst Mon Jun 16 12:45:22 2008
@@ -57,4 +57,4 @@
interface, including cutting planes and projections. (More on those later!)::
>>> pc.add_projection("Temperature", 0, weight_field="CellMass")
- >>> pc.add_threephase_sphere(1.0, 'pc', ["Density","Temperature","H2I_Fraction"])
+ >>> pc.add_phase_sphere(1.0, 'pc', ["Density","Temperature","H2I_Fraction"])
Modified: trunk/doc/source/tutorial/basic_objects.rst
==============================================================================
--- trunk/doc/source/tutorial/basic_objects.rst (original)
+++ trunk/doc/source/tutorial/basic_objects.rst Mon Jun 16 12:45:22 2008
@@ -3,14 +3,6 @@
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.
-
-.. index:: derivedfield, indices
-
Derived Fields and Indices
--------------------------
@@ -32,6 +24,10 @@
>>> print my_grid["Density"][0,:,4]
>>> print my_grid["Density"][0,2:4,4]
+The first will return to us everything where the x index is zero and the z
+index is four. The second will return the same, except restrict the return to
+only between indices 2 and 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
@@ -63,11 +59,18 @@
used implicity with plotting (more on that later) and not very often from
the interpreter.
-Data Regions
-------------
+Boxes
+-----
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.::
>>> my_region = a.h.region([0.5,0.5,0.5], [0.0,0.0,0.0], [1.0,1.0,1.0])
+
+This data object will respect a fixed protocol, as will all the 3D objects.
+You ask it for a field, and it returns that field: ::
+
+ >>> my_region["Density"]
+
+We'll talk more about which fields are available in the next section.
Modified: trunk/doc/source/tutorial/derived_fields.rst
==============================================================================
--- trunk/doc/source/tutorial/derived_fields.rst (original)
+++ trunk/doc/source/tutorial/derived_fields.rst Mon Jun 16 12:45:22 2008
@@ -19,7 +19,7 @@
Defining Simple Fields
----------------------
-There are LOTS! Not only that, but you can set up your own fields, too,
+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.::
Modified: trunk/doc/source/tutorial/getting_started.rst
==============================================================================
--- trunk/doc/source/tutorial/getting_started.rst (original)
+++ trunk/doc/source/tutorial/getting_started.rst Mon Jun 16 12:45:22 2008
@@ -24,22 +24,35 @@
>>> import yt.lagos as lagos
+The :mod:`yt.lagos` module is now in our namespace and called :mod:`lagos`; you
+can import it as whatever you like, but we'll stick with that for the remainder
+of the tutorial. Let's move on to opening an output.
+
.. index:: hierarchy
The Hierarchy
-------------
-We first instantiate a StaticOutput. This is a pretty simple process - lagos
+We first instantiate a StaticOutput, which is a single disk-written timestep of
+the simulation This is a pretty simple process - :mod:`lagos`
will grab the parameter file that you give it, parse it, set up some handy
units, and then return control to you.::
- >>> a = lagos.EnzoStaticOutput("/Users/matthewturk/Research/data/DataDir0036/DataDump0036")
+ >>> a = lagos.EnzoStaticOutput("my_data0001.dir/my_data0001")
But what good is just a parameter file? What we really want is to be able to
manipulate the grids, and all the fields stored in those grids. Fortunately,
we can access the hierarchy as either 'hierarchy' or 'h'.
-Let's start out by finding the location of the maximum Density.
+
+The 'h' property will instantiate an :class:`EnzoHierarchy` object, which
+posseses information about the grids in a given output, as well as their
+spatial relationships to each other. Furthermore, :mod:`yt` will store
+commonly-used and expensive-to-generate data in an HDF5 file associated with
+that object -- things like projections, 3D phase profiles, and so on.
+
+All of the data-handling we want to do will be mediated by the hierarchy file;
+so let's start out by finding the location of the maximum Density.
Note that here we use an inline-unpacking -- find_max returns two values,
packed into a tuple, so we manually unpack them right here.::
@@ -49,13 +62,18 @@
.. index:: Grid, 3ddata;grid
+Now we know where the maximum density is located, and what it is. This is a
+pretty simple process, and we will use it later to center spheres and boxes and
+disks on the point of maximum density.
+
+
The Grids
---------
The hierarchy object has some interesting methods that let us access the data
in different ways. Let's start by looking at the grids. ::
- >>> my_grid = a.h.grids[0] # The root grid
+ >>> my_grid = a.h.grids[0] # The first grid in the hierarchy
>>> print my_grid.dx, my_grid.ActiveDimensions # Some of the attributes
@@ -64,7 +82,6 @@
>>> print dir(my_grid)
-
In general, a method or property that begins with '_' is not meant to be
called directly, and '__' means that it definitely shouldn't be called by an
external process.
@@ -74,4 +91,12 @@
>>> print my_grid["Density"]*my_grid["Temperature"]
+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. In the
+next section we'll take about the difference between a native field and a
+derived field.
+.. index:: derivedfield, indices
Modified: trunk/doc/source/tutorial/index.rst
==============================================================================
--- trunk/doc/source/tutorial/index.rst (original)
+++ trunk/doc/source/tutorial/index.rst Mon Jun 16 12:45:22 2008
@@ -18,5 +18,4 @@
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 Jun 16 12:45:22 2008
@@ -2,7 +2,7 @@
========
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,
+of one or more variables, along one, two or three different dimensions. For example,
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.
@@ -46,6 +46,9 @@
>>> pylab.ylabel(r"$\rm{Density} (\rm{g}/\rm{cm}^3)$")
>>> pylab.savefig("my_profile.png")
+Note that we manually plot it, but :mod:`raven` also includes an automated
+plotting method for obtaining and displaying radial profiles.
+
Two-Dimensional Profiles
------------------------
@@ -57,3 +60,59 @@
>>> prof2d.add_fields("CellVolume", weight=None)
>>> pylab.pcolormesh(prof2d["Density"], prof2d["Temperature"],
... prof2d["CellVolume"].transpose())
+
+Again, we have manually plotted this, but an automated plotter is available.::
+
+ >>> pc = raven.PlotCollection(a)
+ >>> pc.add_phase_object(sphere, ["Density", "Temperature", "x-velocity"],
+ ... 16, True, (1e-32, 1e-24),
+ ... 16, True, (1e2, 1e5), lazy_reader=True)
+
+The API is slightly different here, but it will accept any object (a sphere in
+our case) and generate the profile based on the arguments. If you simply want
+a sphere, you can ask for that and the sphere will be generated as well -- and
+the function will automatically generate the bounds. (Although, keep in mind,
+if you do not supply bounds it will have to read the data into memory, which
+means you are no longer able to use the :keyword:`lazy_reader` functionality.
+This will change in future versions.) ::
+
+
+ >>> pc.add_phase_sphere(0.1, 'kpc', ["Density", "Temperature", "x-velocity"])
+
+Three-Dimensional Profiles
+--------------------------
+
+.. image:: ../_images/example_3dphase.png
+ :align: left
+ :width: 250
+
+If you have the `S2PLOT <http://astronomy.swin.edu.au/s2plot/index.php?title=S2PLOT>`_
+bindings installed, you can visualize three-dimensional profiles with yt. The
+API is nearly identical to that used to generate the lower-dimensionality
+profiles. ::
+
+ >>> prof = lagos.BinnedProfile3D(sphere,
+ ... 128, "Density", extrema[0][0], extrema[0][1], True,
+ ... 128, "Temperature", extrema[1][0], extrema[1][1], True,
+ ... 128, "z-velocity", extrema[2][0], extrema[2][1], True,
+ ... lazy_reader=True)
+ >>> prof.add_fields("CellMassMsun", None)
+
+I've wrapped the bounds into the variable *extrema*, to make it more clear.
+Once you have this profile, you can plot it with S2PLOT by calling initializing
+a 3D plot and calling :func:`run`. ::
+
+ >>> vrc = raven.VolumeRendering3DProfile(k, "CellMassMsun", amax=1.0)
+ >>> vrc.run()
+
+They can be generated anywhere -- and serialized -- so if you want to generate
+them on a remote machine and use a local-machine for display, you only have to
+call :func:`store` and then initialize, instead of the standard
+:class:`BinnedProfile3D`, :class:`StoredBinnedProfile3D`. ::
+
+ >>> prof.store_profile('MyProfile')
+ >>> new_prof = lagos.StoredBinnedProfile3D(a, 'MyProfile')
+
+The retrieved profile is static, and new data cannot be added. However, it
+becomes useful in the likely circumstance that your data is stored on a machine
+on which is inconvenient to do OpenGL-based data exploration.
Added: trunk/doc/wipe_svn.sh
==============================================================================
--- (empty file)
+++ trunk/doc/wipe_svn.sh Mon Jun 16 12:45:22 2008
@@ -0,0 +1,18 @@
+for ext in txt html css png js doctree pickle json
+do
+ find build/ -name "*.${ext}" -exec rm -v {} \;
+done
+
+PYTHONPATH=$HOME/Development/yt/trunk/
+make html
+
+echo "Files deleted since last svn commit:"
+echo
+svn stat | grep \!
+echo
+
+echo "Files added since last svn commit:"
+echo " (generated with 'svn stat | grep \? )'"
+echo
+svn stat | grep \?
+echo
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