plastid.util.io.binary module

Tools for reading values from binary files

See Also

struct

Binary data structures in Python

class plastid.util.io.binary.BinaryParserFactory(name, fmt, fields)

Bases: object

Parser factory for different types of binary records.

Creates parsers that unpack binary byte streams into dictionaries that match field names to values. These parsers are most useful as components of binary file readers.

Parameters

namestr

Name for parser

fmtstr

String specifying binary format of data. See struct

fieldslist

Ordered list of field names to bind to data unpacked from binary file

See also

struct

For information on format strings

Examples

A binary RGB color parser:

>>> ColorParser = BinaryParserFactory("ColorParser","3Q",["r","g","b"])
>>> fh = open("some_binary_file_containing_colors.bin","rb") # 'b' is important in mode flag!!
>>> fh.seek(byte_location_of_an_rgb_color)
>>> rgb_dict = ColorParser(fh) # read and parse 3 8-bit integers from file
>>> rgb_dict
    { "r" : 255,
      "g" : 0,
      "b" : 52 }

Attributes

namestr

Human-readable name for parser

fmtstr

String specifying binary format of data, as specified in struct

fieldslist

List of strings specifying variable names to bind to data when unpacked from a binary file, in same order as items in fmt

ntnamedtuple

A namedtuple instance that will provide names to the unpacked data

Methods

__call__(fh[, byte_order])	Parse data from fh into a dictionary mapping field names to their values
calcsize([byte_order])	Return calculated size, in bytes, of record

calcsize(byte_order='<')

Return calculated size, in bytes, of record

Parameters

byte_orderstr

Character indicating endian-ness of data (default: ‘<’ for little-endian)

Returns

int

Calculated size of record, in bytes

plastid.util.io.binary.find_null_bytes(inp, null=b'\x00')

Finds all null characters in a byte-formatted input string

Parameters

inpbytes (or str in Python 2.7)

byte string

Returns

numpy.ndarray

numpy array of integers indexing where the null character ** was found