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table.py
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table.py
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# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement Table."""
from abc import ABCMeta, abstractmethod
import copy
from numbers import Integral
from math import log10
from sys import stdout
from hoomd.write.custom_writer import _InternalCustomWriter
from hoomd.custom.custom_action import _InternalAction
from hoomd.logging import LoggerCategories, Logger
from hoomd.data.parameterdicts import ParameterDict
from hoomd.data.typeconverter import OnlyTypes
from hoomd.util import dict_flatten
from hoomd.custom import Action
class _OutputWriter(metaclass=ABCMeta):
"""Represents the necessary functions for writing out data.
We use this to ensure the output object passed to Table will support the
necessary functions.
"""
@abstractmethod
def flush(self):
pass
@abstractmethod
def write(self):
pass
@abstractmethod
def writable(self):
pass
@classmethod
def __subclasshook__(cls, C):
if cls is _OutputWriter:
return all(hasattr(C, method) for method in cls.__abstractmethods__)
else:
return NotImplemented
def _ensure_writable(fh):
if not fh.writable():
raise ValueError("file-like object must be writable.")
return fh
class _Formatter:
"""Internal class for number and string formatting for Table object.
Main method is ``__call__``. It takes a value with the corresponding column
width and outputs the string to use for that column. Some of these
parameters are not currently used in the _InternalTable class, but are
available in the _Formatter class, meaning that adding these features later
would be fairly simple. I (Brandon Butler) did not think they were worth
complicating the Table Logger any more than it currently is though, so they
are not used now.
Args:
pretty (bool): whether to attempt to make output pretty (more readable).
max_precision (int): The max length for formatting a number or string.
max_decimals_pretty (int): The maximum number of decimals. This is
required to ensure that the decimals don't eat up all space in a
pretty print.
pad (str, optional): What to pad extra column space with, defaults to
space.
align (str, optional): What type of alignment to use, defaults to
centered ('^').
"""
def __init__(self,
pretty=True,
max_precision=15,
max_decimals_pretty=5,
pad=" ",
align="^"):
self.generate_fmt_strings(pad, align)
self.pretty = pretty
self.precision = max_precision - 1
self.max_decimals_pretty = max_decimals_pretty
def generate_fmt_strings(self, pad, align):
base = "{:" + pad + align
self._num_format = base + "{width}{type}}"
self._str_format = base + "{width}}"
def __call__(self, value, column_width):
if isinstance(value, str):
return self.format_str(value, column_width)
else:
return self.format_num(value, column_width)
def format_num(self, value, column_width):
# Always output full integer values
if isinstance(value, Integral):
return self._num_format.format(value, width=column_width, type="d")
# For floating point numbers
else:
# The minimum length representation if greater than one than the
# smallest representation is to write the number without any
# infomration past the decimal point. For values less than 1 the
# smallest is 0.xxx. The plus one is for the decimal point. We
# already attempt to print out as many decimal points as possible so
# we only need to determine the minumum size to the left of the
# decimal point including the decimal point.
min_len_repr = int(log10(max(abs(value), 1))) + 1
if value < 0:
min_len_repr += 1 # add 1 for the negative sign
# Use scientific formatting
if not min_len_repr < 6 or min_len_repr > column_width:
# Determine the number of decimals to use
if self.pretty:
decimals = min(max(column_width - 6, 1),
self.max_decimals_pretty)
else:
decimals = max(self.precision, 0)
type_fmt = "." + str(decimals) + "e"
# Use regular formatting
else:
# Determine the number of decimals to use
if self.pretty:
decimals = min(max(column_width - min_len_repr - 2, 1),
self.max_decimals_pretty)
else:
decimals = max(self.precision - min_len_repr + 1, 0)
type_fmt = "." + str(decimals) + "f"
return self._num_format.format(value,
width=column_width,
type=type_fmt)
def format_str(self, value, column_width):
if self.pretty and len(value) > column_width:
truncate_to = max(1, column_width - 2)
return self._str_format.format(value[-truncate_to:],
width=column_width)
else:
return self._str_format.format(value, width=column_width)
def __eq__(self, other):
if not isinstance(other, _Formatter):
return NotImplemented
return (self.pretty == other.pretty
and self.precision == other.precision
and self.max_decimals_pretty == other.max_decimals_pretty
and self._num_format == other._num_format
and self._str_format == other._str_format)
class _TableInternal(_InternalAction):
"""Implements the logic for a simple text based logger backend.
This currently has to check the logged quantities every time to ensure it
has not changed since the last run of `~.act`. Performance could be
improved by allowing for writing of data without checking for a change in
logged quantities, but would be more fragile.
"""
_invalid_logger_categories = LoggerCategories.any([
'sequence', 'object', 'particle', 'bond', 'angle', 'dihedral',
'improper', 'pair', 'constraint', 'strings'
])
flags = [
Action.Flags.ROTATIONAL_KINETIC_ENERGY, Action.Flags.PRESSURE_TENSOR,
Action.Flags.EXTERNAL_FIELD_VIRIAL
]
_skip_for_equality = {"_comm"}
def __init__(self,
logger,
output=stdout,
header_sep='.',
delimiter=' ',
pretty=True,
max_precision=10,
max_header_len=None):
param_dict = ParameterDict(header_sep=str,
delimiter=str,
min_column_width=int,
max_header_len=OnlyTypes(int,
allow_none=True),
pretty=bool,
max_precision=int,
output=OnlyTypes(
_OutputWriter,
postprocess=_ensure_writable),
logger=Logger)
param_dict.update(
dict(header_sep=header_sep,
delimiter=delimiter,
min_column_width=max(10, max_precision + 6),
max_header_len=max_header_len,
max_precision=max_precision,
pretty=pretty,
output=output,
logger=logger))
self._param_dict = param_dict
# internal variables that are not part of the state.
# Ensure that only scalar and potentially string are set for the logger
if (LoggerCategories.scalar not in logger.categories
or logger.categories & self._invalid_logger_categories
!= # noqa: W504 (yapf formats this incorrectly
LoggerCategories.NONE):
raise ValueError(
"Given Logger must have the scalar categories set.")
self._cur_headers_with_width = dict()
self._fmt = _Formatter(pretty, max_precision)
self._comm = None
def _setattr_param(self, attr, value):
"""Makes self._param_dict attributes read only."""
raise ValueError("Attribute {} is read-only.".format(attr))
def attach(self, simulation):
self._comm = simulation.device._comm
def detach(self):
self._comm = None
def _get_log_dict(self):
"""Get a flattened dict for writing to output."""
return {
key: value[0]
for key, value in dict_flatten(self.logger.log()).items()
}
def _update_headers(self, new_keys):
"""Update headers and write the current headers to output.
This function could be made simpler and faster by moving some of the
transformation to act. Since we don't expect the headers to change often
however, this would likely slow the writer down. The design is to
off-load any potnentially unnecessary calculations to this function even
if that means more overall computation when headers change.
"""
header_output_list = []
header_dict = {}
for namespace in new_keys:
header = self._determine_header(namespace, self.header_sep,
self.max_header_len)
column_size = max(len(header), self.min_column_width)
header_dict[namespace] = column_size
header_output_list.append((header, column_size))
self._cur_headers_with_width = header_dict
self.output.write(
self.delimiter.join((self._fmt.format_str(hdr, width)
for hdr, width in header_output_list)))
self.output.write('\n')
@staticmethod
def _determine_header(namespace, sep, max_len):
if max_len is None:
return sep.join(namespace)
else:
index = -1
char_count = len(namespace[-1])
for name in reversed(namespace[:-1]):
char_count += len(name)
if char_count > max_len:
break
index -= 1
return sep.join(namespace[index:])
def _write_row(self, data):
"""Write a row of data to output."""
headers = self._cur_headers_with_width
self.output.write(
self.delimiter.join(
(self._fmt(data[k], headers[k]) for k in headers)))
self.output.write('\n')
def act(self, timestep=None):
"""Write row to designated output.
Will also write header when logged quantities are determined to have
changed.
"""
output_dict = self._get_log_dict()
if self._comm is not None and self._comm.rank == 0:
# determine if a header needs to be written. This is always the case
# for the first call of act, and if the logged quantities change
# within a run.
new_keys = output_dict.keys()
if new_keys != self._cur_headers_with_width.keys():
self._update_headers(new_keys)
# Write the data and flush. We must flush to ensure that the data
# isn't merely stored in Python ready to be written later.
self._write_row(output_dict)
self.output.flush()
def __getstate__(self):
state = copy.copy(self.__dict__)
state.pop('_comm', None)
# This is to handle when the output specified is just stdout. By default
# file objects like this are not picklable, so we need to handle it
# differently. We let `None` represent stdout in the state dictionary.
# Most other file like objects will simply fail to be pickled here.
if self.output == stdout:
param_dict = ParameterDict()
param_dict.update(state['_param_dict'])
state['_param_dict'] = param_dict
del state['_param_dict']['output']
state['_param_dict']['output'] = None
return state
else:
return super().__getstate__()
def __setstate__(self, state):
if state['_param_dict']['output'] is None:
del state['_param_dict']['output']
state['_param_dict']['output'] = stdout
state['_param_dict']._type_converter['output'] = OnlyTypes(
_OutputWriter, postprocess=_ensure_writable),
self.__dict__ = state
class Table(_InternalCustomWriter):
"""A delimiter separated value file backend for a Logger.
This can serve as a way to output scalar simulation data to standard out.
However, this is useable to store simulation scalar data to a file as well.
Note:
This only works with scalar and string quantities. If using string
quantities, keep in mind that the default space delimiter will make
strings with spaces in them will cause read errors if attempting to read
the outputed data with a space delimited file reader.
Note:
All attributes for this class are static. They cannot be set to new
values once created.
Args:
trigger (hoomd.trigger.Trigger): The trigger to determine when to run
the Table back end.
logger (hoomd.logging.Logger): The logger to query for output. The
'scalar' categories must be set on the logger, and the 'string'
categories is optional.
output (``file-like`` object , optional): A file-like object to output
the data from, defaults to standard out. The object must have write
and flush methods and a mode attribute.
header_sep (`str`, optional): String to use to separate names in
the logger's namespace, defaults to '.'. For example, if logging the
total energy of an `hoomd.md.pair.LJ` pair force object, the default
header would be ``md.pair.LJ.energy`` (assuming that
``max_header_len`` is not set).
delimiter (`str`, optional): String used to separate elements in
the space delimitated file, defaults to ' '.
pretty (`bool`, optional): Flags whether to attempt to make output
prettier and easier to read, defaults to True. To make the ouput
easier to read, the output will compromise on outputted precision
for improved readability. In many cases, though the precision will
still be high with pretty set to ``True``.
max_precision (`int`, optional): If pretty is not set, then this
controls the maximum precision to use when outputing numerical
values, defaults to 10.
max_header_len (`int`, optional): If not None (the default), limit
the outputted header names to length ``max_header_len``. When not
None, names are grabbed from the most specific to the least. For
example, if set to 7 the namespace 'hoomd.md.pair.LJ.energy' would
be set to 'energy'. Note that at least the most specific part of the
namespace will be used regardless of this setting (e.g. if set to 5
in the previous example, 'energy' would still be the header).
Attributes:
trigger (hoomd.trigger.Trigger): The trigger to determine when to run
the Table back end.
logger (hoomd.logging.Logger): The logger to query for output. The
'scalar' categories must be set on the logger, and the 'string'
categories is optional.
output (``file-like`` object): A file-like object to output
the data from. The object must have write and flush methods and a
mode attribute.
header_sep (str): String to use to separate names in
the logger's namespace.'. For example, if logging the total energy
of an `hoomd.md.pair.LJ` pair force object, the default header would
be ``md.pair.LJ.energy`` (assuming that ``max_header_len`` is not
set).
delimiter (str): String used to separate elements in the space
delimitated file.
pretty (bool): Flags whether to attempt to make output
prettier and easier to read. To make the ouput easier to read, the
output will compromise on outputted precision for improved
readability. In many cases, though the precision will still be high
with pretty set to ``True``.
max_precision (`int`, optional): If pretty is not set, then this
controls the maximum precision to use when outputing numerical
values, defaults to 10.
max_header_len (int): Limits the outputted header names to length
``max_header_len`` when not ``None``. Names are grabbed from the
most specific to the least. For example, if set to 7 the namespace
'hoomd.md.pair.LJ.energy' would be set to 'energy'. Note that at
least the most specific part of the namespace will be used
regardless of this setting (e.g. if set to 5 in the previous
example, 'energy' would still be the header).
min_column_width (int): The minimum allowed column width.
"""
_internal_class = _TableInternal
def write(self):
"""Write out data to ``self.output``.
Writes a row from given ``hoomd.logging.Logger`` object data.
"""
self._action.act()