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800 lines (683 loc) · 27.8 KB
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import pickle
import re
import sys
import warnings
from typing import Iterable, Optional, Tuple, List, Generator, Callable, Any
from ast import literal_eval
from collections import OrderedDict
from functools import lru_cache
from itertools import chain, repeat
from math import isnan
from os import path, remove
from fnmatch import fnmatch
from glob import glob
import numpy as np
from Orange.data import Table, Domain, Variable, DiscreteVariable, \
StringVariable, ContinuousVariable, TimeVariable
from Orange.data.io_util import Compression, open_compressed, \
isnastr, guess_data_type, sanitize_variable
from Orange.data.util import get_unique_names_duplicates
from Orange.data.variable import VariableMeta
from Orange.misc.collections import natural_sorted
from Orange.util import Registry, flatten, namegen
__all__ = ["FileFormatBase", "Flags", "DataTableMixin", "PICKLE_PROTOCOL"]
PICKLE_PROTOCOL = 4
class Flags:
"""Parser for column flags (i.e. third header row)"""
DELIMITER = ' '
_RE_SPLIT = re.compile(r'(?<!\\)' + DELIMITER).split
_RE_ATTR_UNQUOTED_STR = re.compile(r'^[a-zA-Z_]').match
ALL = OrderedDict((
('class', 'c'),
('ignore', 'i'),
('meta', 'm'),
('weight', 'w'),
('.+?=.*?', ''), # general key=value attributes
))
_RE_ALL = re.compile(r'^({})$'.format('|'.join(
filter(None, flatten(ALL.items())))))
def __init__(self, flags):
for v in filter(None, self.ALL.values()):
setattr(self, v, False)
self.attributes = {}
for flag in flags or []:
flag = flag.strip()
if self._RE_ALL.match(flag):
if '=' in flag:
k, v = flag.split('=', 1)
if not Flags._RE_ATTR_UNQUOTED_STR(v):
try:
v = literal_eval(v)
except SyntaxError:
# If parsing failed, treat value as string
pass
self.attributes[k] = v
else:
setattr(self, flag, True)
setattr(self, self.ALL.get(flag, ''), True)
elif flag:
warnings.warn('Invalid attribute flag \'{}\''.format(flag))
@staticmethod
def join(iterable, *args):
return Flags.DELIMITER.join(i.strip().replace(Flags.DELIMITER,
'\\' + Flags.DELIMITER)
for i in chain(iterable, args)).lstrip()
@staticmethod
def split(s):
return [i.replace('\\' + Flags.DELIMITER, Flags.DELIMITER)
for i in Flags._RE_SPLIT(s)]
# Matches discrete specification where all the values are listed, space-separated
_RE_DISCRETE_LIST = re.compile(r'^\s*[^\s]+(\s[^\s]+)+\s*$')
_RE_TYPES = re.compile(r'^\s*({}|{}|)\s*$'.format(
_RE_DISCRETE_LIST.pattern,
'|'.join(flatten(getattr(vartype, 'TYPE_HEADERS')
for vartype in Variable.registry.values()))
))
_RE_FLAGS = re.compile(r'^\s*( |{}|)*\s*$'.format(
'|'.join(flatten(filter(None, i) for i in Flags.ALL.items()))
))
class _ColumnProperties:
def __init__(self, valuemap=None, values=None, orig_values=None,
coltype=None, coltype_kwargs=None):
self.valuemap = valuemap
self.values = values
self.orig_values = orig_values
self.coltype = coltype
if coltype_kwargs is None:
self.coltype_kwargs = {}
else:
self.coltype_kwargs = dict(coltype_kwargs)
class _TableHeader:
"""
Contains functions for table header construction (and its data).
"""
HEADER1_FLAG_SEP = '#'
def __init__(self, headers: List):
"""
Parameters
----------
headers: List
Header rows, to be used for constructing domain.
"""
names, types, flags = self.create_header_data(headers)
self.names = get_unique_names_duplicates(names)
self.types = types
self.flags = flags
@classmethod
def create_header_data(cls, headers: List) -> Tuple[List, List, List]:
"""
Consider various header types (single-row, two-row, three-row, none).
Parameters
----------
headers: List
Header rows, to be used for constructing domain.
Returns
-------
names: List
List of variable names.
types: List
List of variable types.
flags: List
List of meta info (i.e. class, meta, ignore, weights).
"""
return {3: lambda x: x,
2: cls._header2,
1: cls._header1}.get(len(headers), cls._header0)(headers)
@classmethod
def _header2(cls, headers: List[List[str]]) -> Tuple[List, List, List]:
names, flags = headers
return names, cls._type_from_flag(flags), cls._flag_from_flag(flags)
@classmethod
def _header1(cls, headers: List[List[str]]) -> Tuple[List, List, List]:
"""
First row format either:
1) delimited column names
2) -||- with type and flags prepended, separated by #,
e.g. d#sex,c#age,cC#IQ
"""
flags, names = zip(*[i.split(cls.HEADER1_FLAG_SEP, 1)
if cls.HEADER1_FLAG_SEP in i else ('', i)
for i in headers[0]])
names = list(names)
return names, cls._type_from_flag(flags), cls._flag_from_flag(flags)
@classmethod
def _header0(cls, _) -> Tuple[List, List, List]:
# Use heuristics for everything
return [], [], []
@staticmethod
def _type_from_flag(flags: List[str]) -> List[str]:
return [''.join(filter(str.isupper, flag)).lower() for flag in flags]
@staticmethod
def _flag_from_flag(flags: List[str]) -> List[str]:
return [Flags.join(filter(str.islower, flag)) for flag in flags]
class _TableBuilder:
X_ARR, Y_ARR, M_ARR, W_ARR = range(4)
DATA_IND, DOMAIN_IND, TYPE_IND = range(3)
def __init__(self, data: np.ndarray, ncols: int,
header: _TableHeader, offset: int):
self.data = data
self.ncols = ncols
self.header = header
self.offset = offset
self.namegen: Generator[str] = namegen('Feature ', 1)
self.cols_X: List[np.ndarray] = []
self.cols_Y: List[np.ndarray] = []
self.cols_M: List[np.ndarray] = []
self.cols_W: List[np.ndarray] = []
self.attrs: List[Variable] = []
self.clses: List[Variable] = []
self.metas: List[Variable] = []
def create_table(self) -> Table:
self.create_columns()
if not self.data.size:
return Table.from_domain(self.get_domain(), 0)
else:
return Table.from_numpy(self.get_domain(), *self.get_arrays())
def create_columns(self):
names = self.header.names
types = self.header.types
for col in range(self.ncols):
flag = Flags(Flags.split(self.header.flags[col]))
if flag.i:
continue
type_ = types and types[col].strip()
creator = self._get_column_creator(type_)
column = creator(self.data, col, values=type_, offset=self.offset)
self._take_column(names and names[col], column, flag)
self._reclaim_memory(self.data, col)
@classmethod
def _get_column_creator(cls, type_: str) -> Callable:
if type_ in StringVariable.TYPE_HEADERS:
return cls._string_column
elif type_ in ContinuousVariable.TYPE_HEADERS:
return cls._cont_column
elif type_ in TimeVariable.TYPE_HEADERS:
return cls._time_column
elif _RE_DISCRETE_LIST.match(type_):
return cls._disc_with_vals_column
elif type_ in DiscreteVariable.TYPE_HEADERS:
return cls._disc_no_vals_column
else:
return cls._unknown_column
@staticmethod
def _string_column(data: np.ndarray, col: int, **_) -> _ColumnProperties:
vals, _ = _TableBuilder._values_mask(data, col)
return _ColumnProperties(values=vals, coltype=StringVariable,
orig_values=vals)
@staticmethod
def _cont_column(data: np.ndarray, col: int,
offset=0, **_) -> _ColumnProperties:
orig_vals, namask = _TableBuilder._values_mask(data, col)
values = np.empty(data.shape[0], dtype=float)
try:
np.copyto(values, orig_vals, casting="unsafe", where=~namask)
values[namask] = np.nan
except ValueError:
row = 0
for row, num in enumerate(orig_vals):
if not isnastr(num):
try:
float(num)
except ValueError:
break
raise ValueError(f'Non-continuous value in (1-based) '
f'line {row + offset + 1}, column {col + 1}')
return _ColumnProperties(values=values, coltype=ContinuousVariable,
orig_values=orig_vals)
@staticmethod
def _time_column(data: np.ndarray, col: int, **_) -> _ColumnProperties:
vals, namask = _TableBuilder._values_mask(data, col)
return _ColumnProperties(values=np.where(namask, "", vals),
coltype=TimeVariable, orig_values=vals)
@staticmethod
def _disc_column(data: np.ndarray, col: int) -> \
Tuple[np.ndarray, VariableMeta]:
vals, namask = _TableBuilder._values_mask(data, col)
return np.where(namask, "", vals), DiscreteVariable
@staticmethod
def _disc_no_vals_column(data: np.ndarray, col: int, **_) -> \
_ColumnProperties:
vals, coltype = _TableBuilder._disc_column(data, col)
return _ColumnProperties(valuemap=natural_sorted(set(vals) - {""}),
values=vals, coltype=coltype,
orig_values=vals)
@staticmethod
def _disc_with_vals_column(data: np.ndarray, col: int,
values="", **_) -> _ColumnProperties:
vals, coltype = _TableBuilder._disc_column(data, col)
return _ColumnProperties(valuemap=Flags.split(values), values=vals,
coltype=coltype, orig_values=vals,
coltype_kwargs={"ordered": True})
@staticmethod
def _unknown_column(data: np.ndarray, col: int, **_) -> _ColumnProperties:
orig_vals, namask = _TableBuilder._values_mask(data, col)
valuemap, values, coltype = guess_data_type(orig_vals, namask)
return _ColumnProperties(valuemap=valuemap, values=values,
coltype=coltype, orig_values=orig_vals)
@staticmethod
def _values_mask(data: np.ndarray, col: int) -> \
Tuple[np.ndarray, np.ndarray]:
try:
values = data[:, col]
except IndexError:
values = np.array([], dtype=object)
return values, isnastr(values)
def _take_column(self, name: Optional[str], column: _ColumnProperties,
flag: Flags):
cols, dom_vars = self._lists_from_flag(flag, column.coltype)
values = column.values
if dom_vars is not None:
if not name:
name = next(self.namegen)
values, var = sanitize_variable(
column.valuemap, values, column.orig_values,
column.coltype, column.coltype_kwargs, name=name)
var.attributes.update(flag.attributes)
dom_vars.append(var)
if isinstance(values, np.ndarray) and not values.flags.owndata:
values = values.copy() # might view `data` (string columns)
cols.append(values)
def _lists_from_flag(self, flag: Flags, coltype: VariableMeta) -> \
Tuple[List, Optional[List]]:
if flag.m or coltype is StringVariable:
return self.cols_M, self.metas
elif flag.w:
return self.cols_W, None
elif flag.c:
return self.cols_Y, self.clses
else:
return self.cols_X, self.attrs
@staticmethod
def _reclaim_memory(data: np.ndarray, col: int):
# allow gc to reclaim memory used by string values
try:
data[:, col] = None
except IndexError:
pass
def get_domain(self) -> Domain:
return Domain(self.attrs, self.clses, self.metas)
def get_arrays(self) -> Tuple[np.ndarray, np.ndarray,
np.ndarray, np.ndarray]:
lists = ((self.cols_X, None),
(self.cols_Y, None),
(self.cols_M, object),
(self.cols_W, float))
X, Y, M, W = [self._list_into_ndarray(lst, dt) for lst, dt in lists]
if X is None:
X = np.empty((self.data.shape[0], 0), dtype=np.float_)
return X, Y, M, W
@staticmethod
def _list_into_ndarray(lst: List, dtype=None) -> Optional[np.ndarray]:
if not lst:
return None
array = np.c_[tuple(lst)]
if dtype is not None:
array.astype(dtype)
else:
assert array.dtype == np.float_
return array
class DataTableMixin:
@classmethod
def data_table(cls, data: Iterable[List[str]],
headers: Optional[List] = None) -> Table:
"""
Return Orange.data.Table given rows of `headers` (iterable of iterable)
and rows of `data` (iterable of iterable).
Basically, the idea of subclasses is to produce those two iterables,
however they might.
If `headers` is not provided, the header rows are extracted from `data`,
assuming they precede it.
Parameters
----------
data: Iterable
File content.
headers: List (Optional)
Header rows, to be used for constructing domain.
Returns
-------
table: Table
Data as Orange.data.Table.
"""
if not headers:
headers, data = cls.parse_headers(data)
header = _TableHeader(headers)
# adjusting data may change header properties
array, n_columns = cls.adjust_data_width(data, header)
builder = _TableBuilder(array, n_columns, header, len(headers))
return builder.create_table()
@classmethod
def parse_headers(cls, data: Iterable[List[str]]) -> Tuple[List, Iterable]:
"""
Return (header rows, rest of data) as discerned from `data`.
Parameters
----------
data: Iterable
File content.
Returns
-------
header_rows: List
Header rows, to be used for constructing domain.
data: Iterable
File content without header rows.
"""
data = iter(data)
header_rows = []
# Try to parse a three-line header
lines = []
try:
lines.append(list(next(data)))
lines.append(list(next(data)))
lines.append(list(next(data)))
except StopIteration:
lines, data = [], chain(lines, data)
if lines:
l1, l2, l3 = lines
# Three-line header if line 2 & 3 match (1st line can be anything)
if cls.__header_test2(l2) and cls.__header_test3(l3):
header_rows = [l1, l2, l3]
else:
lines, data = [], chain((l1, l2, l3), data)
# Try to parse a single-line header
if not header_rows:
try:
lines.append(list(next(data)))
except StopIteration:
pass
if lines:
# Header if none of the values in line 1 parses as a number
if not all(cls.__is_number(i) for i in lines[0]):
header_rows = [lines[0]]
else:
data = chain(lines, data)
return header_rows, data
@staticmethod
def __is_number(item: str) -> bool:
try:
float(item)
except ValueError:
return False
return True
@staticmethod
def __header_test2(items: List) -> bool:
# Second row items are type identifiers
return all(map(_RE_TYPES.match, items))
@staticmethod
def __header_test3(items: List) -> bool:
# Third row items are flags and column attributes (attr=value)
return all(map(_RE_FLAGS.match, items))
@classmethod
def adjust_data_width(cls, data: Iterable, header: _TableHeader) -> \
Tuple[np.ndarray, int]:
"""
Determine maximum row length.
Return data as an array, with width dependent on header size.
Append `names`, `types` and `flags` if shorter than row length.
Parameters
----------
data: Iterable
File content without header rows.
header: _TableHeader
Header lists converted into _TableHeader.
Returns
-------
data: np.ndarray
File content without header rows.
rowlen: int
Number of columns in data.
"""
def equal_len(lst):
nonlocal strip
if len(lst) > rowlen > 0:
lst = lst[:rowlen]
strip = True
elif len(lst) < rowlen:
lst.extend([''] * (rowlen - len(lst)))
return lst
rowlen = max(map(len, (header.names, header.types, header.flags)))
strip = False
# Ensure all data is of equal width in a column-contiguous array
data = [equal_len([s.strip() for s in row])
for row in data if any(row)]
array = np.array(data, dtype=object, order='F')
if strip:
warnings.warn("Columns with no headers were removed.")
# Data may actually be longer than headers were
try:
rowlen = array.shape[1]
except IndexError:
pass
else:
for lst in (header.names, header.types, header.flags):
equal_len(lst)
return array, rowlen
class _FileReader:
@classmethod
def get_reader(cls, filename):
"""Return reader instance that can be used to read the file
Parameters
----------
filename : str
Returns
-------
FileFormat
"""
for ext, reader in cls.readers.items():
# Skip ambiguous, invalid compression-only extensions added on OSX
if ext in Compression.all:
continue
if fnmatch(path.basename(filename), '*' + ext):
return reader(filename)
raise IOError('No readers for file "{}"'.format(filename))
@classmethod
def set_table_metadata(cls, filename, table):
# pylint: disable=bare-except
if isinstance(filename, str) and path.exists(filename + '.metadata'):
try:
with open(filename + '.metadata', 'rb') as f:
table.attributes = pickle.load(f)
# Unpickling throws different exceptions, not just UnpickleError
except:
with open(filename + '.metadata', encoding='utf-8') as f:
table.attributes = OrderedDict(
(k.strip(), v.strip())
for k, v in (line.split(":", 1)
for line in f.readlines()))
class _FileWriter:
@classmethod
def write(cls, filename, data, with_annotations=True):
if cls.OPTIONAL_TYPE_ANNOTATIONS:
return cls.write_file(filename, data, with_annotations)
else:
return cls.write_file(filename, data)
@classmethod
def write_table_metadata(cls, filename, data):
def write_file(fn):
if all(isinstance(key, str) and isinstance(value, str)
for key, value in data.attributes.items()):
with open(fn, 'w', encoding='utf-8') as f:
f.write("\n".join("{}: {}".format(*kv)
for kv in data.attributes.items()))
else:
with open(fn, 'wb') as f:
pickle.dump(data.attributes, f, protocol=PICKLE_PROTOCOL)
if isinstance(filename, str):
metafile = filename + '.metadata'
if getattr(data, 'attributes', None):
write_file(metafile)
elif path.exists(metafile):
remove(metafile)
@staticmethod
def header_names(data):
return ['weights'] * data.has_weights() + \
[v.name for v in chain(data.domain.attributes,
data.domain.class_vars,
data.domain.metas)]
@staticmethod
def header_types(data):
def _vartype(var):
if var.is_continuous or var.is_string:
return var.TYPE_HEADERS[0]
elif var.is_discrete:
return Flags.join(var.values) if var.ordered else \
var.TYPE_HEADERS[0]
raise NotImplementedError
return ['continuous'] * data.has_weights() + \
[_vartype(v) for v in chain(data.domain.attributes,
data.domain.class_vars,
data.domain.metas)]
@staticmethod
def header_flags(data):
return list(chain(
['weight'] * data.has_weights(),
(Flags.join([flag], *('{}={}'.format(*a) for a in
sorted(var.attributes.items())))
for flag, var in chain(zip(repeat(''), data.domain.attributes),
zip(repeat('class'),
data.domain.class_vars),
zip(repeat('meta'), data.domain.metas)))))
@classmethod
def write_headers(cls, write, data, with_annotations=True):
"""`write` is a callback that accepts an iterable"""
write(cls.header_names(data))
if with_annotations:
write(cls.header_types(data))
write(cls.header_flags(data))
@classmethod
def formatter(cls, var):
# type: (Variable) -> Callable[[Variable], Any]
# Return a column 'formatter' function. The function must return
# something that `write` knows how to write
if var.is_time:
return var.repr_val
elif var.is_continuous:
return lambda value: "" if isnan(value) else value
elif var.is_discrete:
return lambda value: "" if isnan(value) else var.values[int(value)]
elif var.is_string:
return lambda value: value
else:
return var.repr_val
@classmethod
def write_data(cls, write, data):
"""`write` is a callback that accepts an iterable"""
vars_ = list(
chain((ContinuousVariable('_w'),) if data.has_weights() else (),
data.domain.attributes,
data.domain.class_vars,
data.domain.metas))
formatters = [cls.formatter(v) for v in vars_]
for row in zip(data.W if data.W.ndim > 1 else data.W[:, np.newaxis],
data.X,
data.Y if data.Y.ndim > 1 else data.Y[:, np.newaxis],
data.metas):
write([fmt(v) for fmt, v in zip(formatters, flatten(row))])
class _FileFormatMeta(Registry):
def __new__(mcs, name, bases, attrs):
newcls = super().__new__(mcs, name, bases, attrs)
# Optionally add compressed versions of extensions as supported
if getattr(newcls, 'SUPPORT_COMPRESSED', False):
new_extensions = list(getattr(newcls, 'EXTENSIONS', ()))
for compression in Compression.all:
for ext in newcls.EXTENSIONS:
new_extensions.append(ext + compression)
if sys.platform in ('darwin', 'win32'):
# OSX file dialog doesn't support filtering on double
# extensions (e.g. .csv.gz)
# https://bugreports.qt.io/browse/QTBUG-38303
# This is just here for OWFile that gets QFileDialog
# filters from FileFormat.readers.keys()
# EDIT: Windows exhibit similar problems:
# while .tab.gz works, .tab.xz and .tab.bz2 do not!
new_extensions.append(compression)
newcls.EXTENSIONS = tuple(new_extensions)
return newcls
@property
def formats(cls):
return cls.registry.values()
@lru_cache(5)
def _ext_to_attr_if_attr2(cls, attr, attr2):
"""
Return ``{ext: `attr`, ...}`` dict if ``cls`` has `attr2`.
If `attr` is '', return ``{ext: cls, ...}`` instead.
If there are multiple formats for an extension, return a format
with the lowest priority.
"""
formats = OrderedDict()
for format_ in sorted(cls.registry.values(), key=lambda x: x.PRIORITY):
if not hasattr(format_, attr2):
continue
for ext in getattr(format_, 'EXTENSIONS', []):
# Only adds if not yet registered
formats.setdefault(ext, getattr(format_, attr, format_))
return formats
@property
def names(cls):
return cls._ext_to_attr_if_attr2('DESCRIPTION', '__class__')
@property
def writers(cls):
return cls._ext_to_attr_if_attr2('', 'write_file')
@property
def readers(cls):
return cls._ext_to_attr_if_attr2('', 'read')
@property
def img_writers(cls):
warnings.warn(
f"'{__name__}.FileFormat.img_writers' is no longer used and "
"will be removed. Please use "
"'Orange.widgets.io.FileFormat.img_writers' instead.",
DeprecationWarning, stacklevel=2
)
return cls._ext_to_attr_if_attr2('', 'write_image')
@property
def graph_writers(cls):
return cls._ext_to_attr_if_attr2('', 'write_graph')
class FileFormatBase(_FileReader, _FileWriter, metaclass=_FileFormatMeta):
# Priority when multiple formats support the same extension. Also
# the sort order in file open/save combo boxes. Lower is better.
PRIORITY = 10000
OPTIONAL_TYPE_ANNOTATIONS = False
@classmethod
def locate(cls, filename, search_dirs=('.',)):
"""Locate a file with given filename that can be opened by one
of the available readers.
Parameters
----------
filename : str
search_dirs : Iterable[str]
Returns
-------
str
Absolute path to the file
"""
if path.exists(filename):
return filename
for directory in search_dirs:
absolute_filename = path.join(directory, filename)
if path.exists(absolute_filename):
break
for ext in cls.readers:
if fnmatch(path.basename(filename), '*' + ext):
break
# glob uses fnmatch internally
matching_files = glob(absolute_filename + ext)
if matching_files:
absolute_filename = matching_files[0]
break
if path.exists(absolute_filename):
break
else:
absolute_filename = ""
if not path.exists(absolute_filename):
raise IOError('File "{}" was not found.'.format(filename))
return absolute_filename
@staticmethod
def open(filename, *args, **kwargs):
"""
Format handlers can use this method instead of the builtin ``open()``
to transparently (de)compress files if requested (according to
`filename` extension). Set ``SUPPORT_COMPRESSED=True`` if you use this.
"""
return open_compressed(filename, *args, **kwargs)
@classmethod
def qualified_name(cls):
return cls.__module__ + '.' + cls.__name__