sfftkrw.core package¶

Parser module¶

parser.py¶

sfftkrw.core.parser.add_args(parser, the_arg)¶

Convenience function to add the_arg to the parser.

This relies on the argument being structured as a dictionary with the keys args for positional arguments and kwargs for the keyword arguments. The value of doing this is that arguments that are reused in several parsers can be referred to by a variable instead of being redefined.

Usage:

>>> my_arg = {'arg': ['-x'], 'kwargs': {'help': 'help'}}
>>> this_parser = argparse.ArgumentParser()
>>> add_args(this_parser, my_arg)

Parameters:	parser (`argparse.ArgumentParser`) – the parser to be modified the_arg (dict) – the argument specified as a dict with keys `args` and `kwargs`
Returns:	a modified parser object
Return type:	`argparse.ArgumentParser`

sfftkrw.core.parser.parse_args(_args, use_shlex=False)¶

Parse and check command-line arguments.

This function does all the heavy lifting in ensuring that commandline arguments are properly formatted and checked for sanity.

In this way command handlers (defined in sfftk/sff.py e.g. handle_convert(...)) assume correct argument values and can concentrate on functionality.

Parameters:	_args (list or str or unicode) – list of arguments (`use_shlex=False`); string of arguments (`use_shlex=True`) use_shlex (bool) – treat `_args` as a string instead for parsing using `shlex` lib
Returns:	parsed arguments
Return type:	`argparse.Namespace`

Printing utilities¶

print_tools.py¶

Utilities for printing stuff to the screen.

sfftkrw.core.print_tools.get_printable_ascii_string(B)¶

Given a bytes string of ASCII and non-ASCII return the maximal printable prefix

Parameters:	B (bytes) – the bytes string to search
Return ascii_b:	the maximal ASCII prefix
Return type:	bytes

sfftkrw.core.print_tools.print_date(print_string, stream=<_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>, newline=True, incl_date=True)¶

Print the given string with date on the given stream

Parameters:	print_string (bytes or str or unicode) – the bytes/str to be printed stream (`sys.stderr` or `sys.stdout`) – the stream/file to write to newline (bool) – whether (default) or not to add a newline at the end incl_date (bool) – whether (default) or not to include the date at the beginning

sfftkrw.core.print_tools.print_static(print_string, stream=<_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>, incl_date=True)¶

Print the given string with date on the given stream from the first position overwriting any characters.

This is a useful way to display progress without overcrowding the screen.

Parameters:	print_string (bytes or str) – the bytes/str to be printed stream (`sys.stderr` or `sys.stdout`) – the stream/file to write to incl_date (bool) – whether (default) or not to include the date at the beginning

Miscellaneous utilities¶

utils.py¶

A collection of helpful utilities

sfftkrw.core.utils.get_path(D, path)¶

Get a path from a dictionary

Parameters:	D (dict) – a dictionary path (list) – an iterable of hashables
Returns:	the item at the path from the dictionary

sfftkrw.core.utils.get_unique_id()¶

Return an ID that will be unique over the current segmentation

Returns:	unique_id
Return type:	int

sfftkrw.core.utils.get_version(fn)¶

Gets the version from the EMDB-SFF file

Parameters:	fn (bytes or unicode) – name of EMDB-SFF file
Returns:	the version
Return type:	unicode

sfftkrw.core.utils.rgba_to_hex(rgba, channels=3)¶

Convert RGB(A) iterable to a hex string (e.g. #aabbcc(dd)

Parameters:	rgba (list or tuple) – an iterable with normalised (values in the closed interval `[0-1]`) colour channel values channels (int) – the number of channels (3 or 4); default 3
Returns:	a hex string
Return type:	str