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Automatically Derived Arrays

Pynbody includes a system which automatically derives one array from others. The idea is that this system

(1) permits analysis code to assume that certain arrays exist -- whether or not they exist in the file;

(2) allows arrays to be kept up-to-date when they depend on other arrays

Built-in derived arrays

The quantities listed under :mod:`~pynbody.derived` are calculated for all simulation types. If you want, for example, to calculate the specific kinetic energy, you can just access the ke array and pynbody will calculate it:

.. ipython::

   In [3]: import pynbody

   In [4]: s = pynbody.load('testdata/g15784.lr.01024.gz')

   In [5]: s['ke']

Note that you cannot directly alter a derived array:

.. ipython:: :okexcept:

   In [5]: s['ke'][0] = 0

But the array updates itself when one of its dependencies changes:

.. ipython::

   In [5]: s['vel']*=2

   In [5]: s['ke']

The recalculation only takes place when required -- in the example above the ke array is stored (just like a normal array) until the velocity array is updated, at which point it is deleted. When you ask for the ke array again, it is recalculated.

This is why you're not allowed to change values in a derived array -- your changes could be overwritten, leading to confusing bugs. However, if you want to make a derived array back into a normal array you can do so.

.. ipython::

   In [5]: s['ke'].derived = False

   In [5]: s['ke'][0] = 0

   In [5]: s['ke']

At this point you've taken full responsibility for the array, so if you update its dependencies the framework won't help you out any longer:

.. ipython::

   In [5]: s['vel']*=2

   In [5]: s['ke']

To get the framework back on your side, you can delete the modified array:

.. ipython::

   In [5]: del s['ke']

   In [5]: s['ke']

Defining your own deriving functions

You can easily define your own derived arrays. The easiest way to do this is using the decorator pynbody.derived_array. An example is given in the :ref:`data access tutorial <create_arrays>`.

When your function is called, the framework monitors any arrays it retrieves from the simulation. It automatically marks the accessed arrays as dependencies for your function.

Built-in derived arrays for all snapshot classes

.. automodule:: pynbody.derived
   :members:

tipsy

Note

These take advantage of arrays present in Gasoline snapshots

.. autofunction:: pynbody.snapshot.tipsy.HII

.. autofunction:: pynbody.snapshot.tipsy.HeIII

.. autofunction:: pynbody.snapshot.tipsy.ne

.. autofunction:: pynbody.snapshot.tipsy.hetot

.. autofunction:: pynbody.snapshot.tipsy.hydrogen

.. autofunction:: pynbody.snapshot.tipsy.feh

.. autofunction:: pynbody.snapshot.tipsy.oxh

.. autofunction:: pynbody.snapshot.tipsy.ofe

.. autofunction:: pynbody.snapshot.tipsy.mgfe

.. autofunction:: pynbody.snapshot.tipsy.nefe

.. autofunction:: pynbody.snapshot.tipsy.sife

.. autofunction:: pynbody.snapshot.tipsy.c_s

.. autofunction:: pynbody.snapshot.tipsy.c_s_turb

.. autofunction:: pynbody.snapshot.tipsy.mjeans

.. autofunction:: pynbody.snapshot.tipsy.mjeans_turb

.. autofunction:: pynbody.snapshot.tipsy.ljeans

.. autofunction:: pynbody.snapshot.tipsy.ljeans_turb

gadget

No special derived quantities at the moment.

Ramses

.. autofunction:: pynbody.snapshot.ramses.mass