Using yt with External Analysis Tools

yt can be used as a glue code between simulation data and other methods of analyzing data. Its facilities for understanding units, disk IO and data selection set it up ideally to use other mechanisms for analyzing, processing and visualizing data.

Calling External Python Codes

Calling external Python codes very straightforward. For instance, if you had a Python code that accepted a set of structured meshes and then post-processed them to apply radiative feedback, one could imagine calling it directly:

import yt
import radtrans

ds = yt.load("DD0010/DD0010")
rt_grids = []

for grid in ds.index.grids:
    rt_grid = radtrans.RegularBox(
         grid.LeftEdge, grid.RightEdge,
         grid["density"], grid["temperature"], grid["metallicity"])
    rt_grids.append(rt_grid)
    grid.clear_data()

radtrans.process(rt_grids)

Or if you wanted to run a population synthesis module on a set of star particles (and you could fit them all into memory) it might look something like this:

import yt
import pop_synthesis

ds = yt.load("DD0010/DD0010")
ad = ds.all_data()
star_masses = ad["StarMassMsun"]
star_metals = ad["StarMetals"]

pop_synthesis.CalculateSED(star_masses, star_metals)

If you have a code that’s written in Python that you are having trouble getting data into from yt, please feel encouraged to email the users list and we’ll help out.

Calling Non-Python External Codes

Independent of its ability to process, analyze and visualize data, yt can also serve as a mechanism for reading and selecting simulation data. In this way, it can be used to supply data to an external analysis routine written in Fortran, C or C++. This document describes how to supply that data, using the example of a simple code that calculates the best axes that describe a distribution of particles as a starting point. (The underlying method is left as an exercise for the reader; we’re only currently interested in the function specification and structs.)

If you have written a piece of code that performs some analysis function, and you would like to include it in the base distribution of yt, we would be happy to do so; drop us a line or see How to Develop yt for more information.

To accomplish the process of linking Python with our external code, we will be using a language called Cython, which is essentially a superset of Python that compiles down to C. It is aware of NumPy arrays, and it is able to massage data between the interpreted language Python and C, Fortran or C++. It will be much easier to utilize routines and analysis code that have been separated into subroutines that accept data structures, so we will assume that our halo axis calculator accepts a set of structs.

Our Example Code

Here is the axes.h file in our imaginary code, which we will then wrap:

typedef struct structParticleCollection {
     long npart;
     double *xpos;
     double *ypos;
     double *zpos;
} ParticleCollection;

void calculate_axes(ParticleCollection *part,
         double *ax1, double *ax2, double *ax3);

There are several components to this analysis routine which we will have to wrap.

  1. We have to wrap the creation of an instance of ParticleCollection.
  2. We have to transform a set of NumPy arrays into pointers to doubles.
  3. We have to create a set of doubles into which calculate_axes will be placing the values of the axes it calculates.
  4. We have to turn the return values back into Python objects.

Each of these steps can be handled in turn, and we’ll be doing it using Cython as our interface code.

Setting Up and Building Our Wrapper

To get started, we’ll need to create two files:

axes_calculator.pyx
axes_calculator_setup.py

These can go anywhere, but it might be useful to put them in their own directory. The contents of axes_calculator.pyx will be left for the next section, but we will need to put some boilerplate code into axes_calculator_setup.pyx. As a quick sidenote, you should call these whatever is most appropriate for the external code you are wrapping; axes_calculator is probably not the best bet.

Here’s a rough outline of what should go in axes_calculator_setup.py:

NAME = "axes_calculator"
EXT_SOURCES = []
EXT_LIBRARIES = ["axes_utils", "m"]
EXT_LIBRARY_DIRS = ["/home/rincewind/axes_calculator/"]
EXT_INCLUDE_DIRS = []
DEFINES = []

from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext

ext_modules = [Extension(NAME,
                 [NAME+".pyx"] + EXT_SOURCES,
                 libraries = EXT_LIBRARIES,
                 library_dirs = EXT_LIBRARY_DIRS,
                 include_dirs = EXT_INCLUDE_DIRS,
                 define_macros = DEFINES)
]

setup(
  name = NAME,
  cmdclass = {'build_ext': build_ext},
  ext_modules = ext_modules
)

The only variables you should have to change in this are the first six, and possibly only the first one. We’ll go through these variables one at a time.

NAME
This is the name of our source file, minus the .pyx. We’re also mandating that it be the name of the module we import. You’re free to modify this.
EXT_SOURCES
Any additional sources can be listed here. For instance, if you are only linking against a single .c file, you could list it here – if our axes calculator were fully contained within a file called calculate_my_axes.c we could link against it using this variable, and then we would not have to specify any libraries. This is usually the simplest way to do things, and in fact, yt makes use of this itself for things like HEALPix and interpolation functions.
EXT_LIBRARIES
Any libraries that will need to be linked against (like m!) should be listed here. Note that these are the name of the library minus the leading lib and without the trailing .so. So libm.so would become m and libluggage.so would become luggage.
EXT_LIBRARY_DIRS
If the libraries listed in EXT_LIBRARIES reside in some other directory or directories, those directories should be listed here. For instance, ["/usr/local/lib", "/home/rincewind/luggage/"] .
EXT_INCLUDE_DIRS
If any header files have been included that live in external directories, those directories should be included here.
DEFINES
Any define macros that should be passed to the C compiler should be listed here; if they just need to be defined, then they should be specified to be defined as “None.” For instance, if you wanted to pass -DTWOFLOWER, you would set this to equal: [("TWOFLOWER", None)].

To build our extension, we would run:

$ python2.7 axes_calculator_setup.py build_ext -i

Note that since we don’t yet have an axes_calculator.pyx, this will fail. But once we have it, it ought to run.

Writing and Calling our Wrapper

Now we begin the tricky part, of writing our wrapper code. We’ve already figured out how to build it, which is halfway to being able to test that it works, and we now need to start writing Cython code.

For a more detailed introduction to Cython, see the Cython documentation at http://docs.cython.org/ . We’ll cover a few of the basics for wrapping code however.

To start out with, we need to open up and edit our file, axes_calculator.pyx. Open this in your favorite version of vi (mine is vim) and we will get started by declaring the struct we need to pass in. But first, we need to include some header information:

import numpy as np
cimport numpy as np
cimport cython
from stdlib cimport malloc, free

These lines simply import and “Cython import” some common routines. For more information about what is already available, see the Cython documentation. For now, we need to start translating our data.

To do so, we tell Cython both where the struct should come from, and then we describe the struct itself. One fun thing to note is that if you don’t need to set or access all the values in a struct, and it just needs to be passed around opaquely, you don’t have to include them in the definition. For an example of this, see the png_writer.pyx file in the yt repository. Here’s the syntax for pulling in (from a file called axes_calculator.h) a struct like the one described above:

cdef extern from "axes_calculator.h":
    ctypedef struct ParticleCollection:
        long npart
        double *xpos
        double *ypos
        double *zpos

So far, pretty easy! We’ve basically just translated the declaration from the .h file. Now that we have done so, any other Cython code can create and manipulate these ParticleCollection structs – which we’ll do shortly. Next up, we need to declare the function we’re going to call, which looks nearly exactly like the one in the .h file. (One common problem is that Cython doesn’t know what const means, so just remove it wherever you see it.) Declare it like so:

void calculate_axes(ParticleCollection *part,
         double *ax1, double *ax2, double *ax3)

Note that this is indented one level, to indicate that it, too, comes from axes_calculator.h. The next step is to create a function that accepts arrays and converts them to the format the struct likes. We declare our function just like we would a normal Python function, using def. You can also use cdef if you only want to call a function from within Cython. We want to call it from Python, too, so we just use def. Note that we don’t here specify types for the various arguments. In a moment we’ll refine this to have better argument types.

def examine_axes(xpos, ypos, zpos):
    cdef double ax1[3], ax2[3], ax3[3]
    cdef ParticleCollection particles
    cdef int i

    particles.npart = len(xpos)
    particles.xpos = <double *> malloc(particles.npart * sizeof(double))
    particles.ypos = <double *> malloc(particles.npart * sizeof(double))
    particles.zpos = <double *> malloc(particles.npart * sizeof(double))

    for i in range(particles.npart):
        particles.xpos[i] = xpos[i]
        particles.ypos[i] = ypos[i]
        particles.zpos[i] = zpos[i]

    calculate_axes(&particles, ax1, ax2, ax3)

    free(particles.xpos)
    free(particles.ypos)
    free(particles.zpos)

    return ( (ax1[0], ax1[1], ax1[2]),
             (ax2[0], ax2[1], ax2[2]),
             (ax3[0], ax3[1], ax3[2]) )

This does the rest. Note that we’ve weaved in C-type declarations (ax1, ax2, ax3) and Python access to the variables fed in. This function will probably be quite slow – because it doesn’t know anything about the variables xpos, ypos, zpos, it won’t be able to speed up access to them. Now we will see what we can do by declaring them to be of array-type before we start handling them at all. We can do that by annotating in the function argument list. But first, let’s test that it works. From the directory in which you placed these files, run:

$ python2.6 setup.py build_ext -i

Now, create a sample file that feeds in the particles:

import axes_calculator
axes_calculator.examine_axes(xpos, ypos, zpos)

Most of the time in that function is spent in converting the data. So now we can go back and we’ll try again, rewriting our converter function to believe that its being fed arrays from NumPy:

def examine_axes(np.ndarray[np.float64_t, ndim=1] xpos,
                 np.ndarray[np.float64_t, ndim=1] ypos,
                 np.ndarray[np.float64_t, ndim=1] zpos):
    cdef double ax1[3], ax2[3], ax3[3]
    cdef ParticleCollection particles
    cdef int i

    particles.npart = len(xpos)
    particles.xpos = <double *> malloc(particles.npart * sizeof(double))
    particles.ypos = <double *> malloc(particles.npart * sizeof(double))
    particles.zpos = <double *> malloc(particles.npart * sizeof(double))

    for i in range(particles.npart):
        particles.xpos[i] = xpos[i]
        particles.ypos[i] = ypos[i]
        particles.zpos[i] = zpos[i]

    calculate_axes(&particles, ax1, ax2, ax3)

    free(particles.xpos)
    free(particles.ypos)
    free(particles.zpos)

    return ( (ax1[0], ax1[1], ax1[2]),
             (ax2[0], ax2[1], ax2[2]),
             (ax3[0], ax3[1], ax3[2]) )

This should be substantially faster, assuming you feed it arrays.

Now, there’s one last thing we can try. If we know our function won’t modify our arrays, and they are C-Contiguous, we can simply grab pointers to the data:

def examine_axes(np.ndarray[np.float64_t, ndim=1] xpos,
                 np.ndarray[np.float64_t, ndim=1] ypos,
                 np.ndarray[np.float64_t, ndim=1] zpos):
    cdef double ax1[3], ax2[3], ax3[3]
    cdef ParticleCollection particles
    cdef int i

    particles.npart = len(xpos)
    particles.xpos = <double *> xpos.data
    particles.ypos = <double *> ypos.data
    particles.zpos = <double *> zpos.data

    for i in range(particles.npart):
        particles.xpos[i] = xpos[i]
        particles.ypos[i] = ypos[i]
        particles.zpos[i] = zpos[i]

    calculate_axes(&particles, ax1, ax2, ax3)

    return ( (ax1[0], ax1[1], ax1[2]),
             (ax2[0], ax2[1], ax2[2]),
             (ax3[0], ax3[1], ax3[2]) )

But note! This will break or do weird things if you feed it arrays that are non-contiguous.

At this point, you should have a mostly working piece of wrapper code. And it was pretty easy! Let us know if you run into any problems, or if you are interested in distributing your code with yt.

A complete set of files is available with this documentation. These are slightly different, so that the whole thing will simply compile, but they provide a useful example.

Exporting Data from yt

yt is installed alongside h5py. If you need to export your data from yt, to share it with people or to use it inside another code, h5py is a good way to do so. You can write out complete datasets with just a few commands. You have to import, and then save things out into a file.

import h5py
f = h5py.File("some_file.h5")
f.create_dataset("/data", data=some_data)

This will create some_file.h5 if necessary and add a new dataset (/data) to it. Writing out in ASCII should be relatively straightforward. For instance:

f = open("my_file.txt", "w")
for halo in halos:
    x, y, z = halo.center_of_mass()
    f.write("%0.2f %0.2f %0.2f\n", x, y, z)
f.close()

This example could be extended to work with any data object’s fields, as well.