nbodykit.io.stack

Classes

FileStack(filetype, path, *args, **kwargs)

A file object that offers a continuous view of a stack of subclasses of FileType instances.
class nbodykit.io.stack.FileStack(filetype, path, *args, **kwargs)[source]

A file object that offers a continuous view of a stack of subclasses of FileType instances.

This allows data to be accessed across multiple files from a single file object. The “stack” is a concatenation of one file to the end of the previous file.

Parameters

  • filetype (subclass of FileType) – the type of file class to initialize

  • path (str) – list of file names, or string specifying single file or containing a glob-like ‘*’ pattern

  • *args – additional arguments to pass to the filetype instance during initialization

  • **kwargs – additional keyword arguments passed to the filetype instance during initialization

Attributes
attrs

Dictionary of meta-data for the stack

columns

A list of the names of the columns in the file.

dtype

A numpy.dtype object holding the data types of each column in the file.

ncol

The number of data columns in the file.

ndim
nfiles

The number of files in the FileStack

shape

The shape of the file, which defaults to (size, )

size

The size of the file, i.e., number of rows

Methods

asarray(self)

Return a view of the file, where the fields of the structured array are stacked in columns of a single numpy array

get_dask(self, column[, blocksize])

Return the specified column as a dask array, which delays the explicit reading of the data until dask.compute() is called

keys(self)

Aliased function to return columns

read(self, columns, start, stop[, step])

Read the specified column(s) over the given range, returning a structured numpy array
__getitem__(self, s)

This function provides numpy-like array indexing of the file object.

It supports:

  1. integer, slice-indexing similar to arrays

  2. string indexing using column names in keys()

  3. array-like indexing using integer lists or boolean arrays

Note

If a single column is being returned, a numpy array holding the data is returned, rather than a structured array with only a single field.

asarray(self)

Return a view of the file, where the fields of the structured array are stacked in columns of a single numpy array

Examples

Start with a file object with three named columns, ra, dec, and z

>>> ff.dtype
dtype([('ra', '<f4'), ('dec', '<f4'), ('z', '<f4')])
>>> ff.shape
(1000,)
>>> ff.columns
['ra', 'dec', 'z']
>>> ff[:3]
array([(235.63442993164062, 59.39099884033203, 0.6225500106811523),
       (140.36181640625, -1.162310004234314, 0.5026500225067139),
       (129.96627807617188, 45.970130920410156, 0.4990200102329254)],
      dtype=(numpy.record, [('ra', '<f4'), ('dec', '<f4'), ('z', '<f4')]))

Select a subset of columns and switch the ordering and convert output to a single numpy array

>>> x = ff[['dec', 'ra']].asarray()
>>> x.dtype
dtype('float32')
>>> x.shape
(1000, 2)
>>> x.columns
['dec', 'ra']
>>> x[:3]
array([[  59.39099884,  235.63442993],
       [  -1.16231   ,  140.36181641],
       [  45.97013092,  129.96627808]], dtype=float32)

Now, select only the first column (dec)

>>> dec = x[:,0]
>>> dec[:3]
array([ 59.39099884,  -1.16231   ,  45.97013092], dtype=float32)
Returns

a file object that will return a numpy array with the columns representing the fields

Return type

FileType

property attrs

Dictionary of meta-data for the stack

property columns

A list of the names of the columns in the file.

This defaults to the named fields in the file’s dtype attribute, but differ from this if a view of the file has been returned with asarray()

property dtype

A numpy.dtype object holding the data types of each column in the file.

get_dask(self, column, blocksize=None)

Return the specified column as a dask array, which delays the explicit reading of the data until dask.compute() is called

The dask array is chunked into blocks of size blocksize

Parameters

  • column (str) – the name of the column to return

  • blocksize (int, optional) – the size of the chunks in the dask array

Returns

the dask array holding the column, which computes the necessary functions to read the data, but delays evaluating until the user specifies

Return type

dask.array.Array

keys(self)

Aliased function to return columns

property ncol

The number of data columns in the file.

property nfiles

The number of files in the FileStack

read(self, columns, start, stop, step=1)[source]

Read the specified column(s) over the given range, returning a structured numpy array

Parameters

  • columns (str, list of str) – the name of the column(s) to return

  • start (int) – the row integer to start reading at

  • stop (int) – the row integer to stop reading at

  • step (int, optional) – the step size to use when reading; default is 1

Returns

data – a numpy structured array holding the requested data

Return type

array_like

property shape

The shape of the file, which defaults to (size, )

Multiple dimensions can be introduced into the shape if a view of the file has been returned with asarray()

property size

The size of the file, i.e., number of rows