nbodykit.io.bigfile

Classes

Automatic
BigFile(path[, exclude, header, dataset]) A file object to handle the reading of columns of data from a bigfile file.
class nbodykit.io.bigfile.BigFile(path, exclude=None, header=<class 'nbodykit.io.bigfile.Automatic'>, dataset='./')[source]

A file object to handle the reading of columns of data from a bigfile file.

bigfile is a reproducible, massively parallel IO library for large, hierarchical datasets, and it is the default format of the FastPM and the MP-Gadget simulations.

See also: https://github.com/rainwoodman/bigfile

Parameters:
  • path (str) – the name of the directory holding the bigfile data
  • exclude (list of str, optional) – the data sets to exlude from loading within bigfile; default is the header. If any list is given, the name of the header column must be given too if it is not part of the data set. The names are shell glob patterns.
  • header (str, or list, optional) – the path to the header; default is to use a column ‘Header’. It is relative to the file, not the dataset. If a list is provided, the attributes is updated from the first entry to the last.
  • dataset (str) – finding columns from a specific dataset in the bigfile; the default is start looking for columns from the root.
Attributes:
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.

shape

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

size

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

Methods

asarray() Return a view of the file, where the fields of the structured array are stacked in columns of a single numpy array
get_dask(column[, blocksize]) Return the specified column as a dask array, which delays the explicit reading of the data until dask.compute() is called
keys() Aliased function to return columns
read(columns, start, stop[, step]) Read the specified column(s) over the given range, as a dictionary
__getitem__(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()

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
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()

dtype

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

get_dask(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()

Aliased function to return columns

ncol

The number of data columns in the file.

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

Read the specified column(s) over the given range, as a dictionary

‘start’ and ‘stop’ should be between 0 and size, which is the total size of the binary file (in particles)

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()

size

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