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import math
from AnyQt.QtWidgets import QFormLayout
from AnyQt.QtCore import Qt
import numpy as np
import sklearn.model_selection as skl
from Orange.widgets import gui
from Orange.widgets.settings import Setting
from Orange.data import Table
from Orange.data.sql.table import SqlTable
from Orange.widgets.utils.localization import pl
from Orange.widgets.utils.widgetpreview import WidgetPreview
from Orange.widgets.widget import Msg, OWWidget, Input, Output
from Orange.util import Reprable
class OWDataSampler(OWWidget):
name = "Data Sampler"
description = "Randomly draw a subset of data points " \
"from the input dataset."
icon = "icons/DataSampler.svg"
priority = 100
category = "Transform"
keywords = "data sampler, random"
_MAX_SAMPLE_SIZE = 2 ** 31 - 1
class Inputs:
data = Input("Data", Table)
class Outputs:
data_sample = Output("Data Sample", Table, default=True)
remaining_data = Output("Remaining Data", Table)
want_main_area = False
resizing_enabled = False
RandomSeed = 42
FixedProportion, FixedSize, CrossValidation, Bootstrap = range(4)
SqlTime, SqlProportion = range(2)
selectedFold: int
use_seed = Setting(True)
replacement = Setting(False)
stratify = Setting(False)
sql_dl = Setting(False)
sampling_type = Setting(FixedProportion)
sampleSizeNumber = Setting(1)
sampleSizePercentage = Setting(70)
sampleSizeSqlTime = Setting(1)
sampleSizeSqlPercentage = Setting(0.1)
number_of_folds = Setting(10)
selectedFold = Setting(1)
# Older versions of the widget had swapped outputs for cross validation
# Migrations set this to True for compability with older workflows
compatibility_mode = Setting(False, schema_only=True)
settings_version = 2
class Information(OWWidget.Information):
compatibility_mode = Msg(
"Compatibility mode\n"
"New versions of widget have swapped outputs for cross validation"
)
class Warning(OWWidget.Warning):
could_not_stratify = Msg("Stratification failed.\n{}")
bigger_sample = Msg('Sample is bigger than input.')
class Error(OWWidget.Error):
too_many_folds = Msg("Number of subsets exceeds data size.")
sample_larger_than_data = Msg("Sample can't be larger than data.")
not_enough_to_stratify = Msg("Data is too small to stratify.")
no_data = Msg("Dataset is empty.")
def __init__(self):
super().__init__()
if self.compatibility_mode:
self.Information.compatibility_mode()
self.data = None
self.indices = None
self.sampled_instances = self.remaining_instances = None
self.sampling_box = gui.vBox(self.controlArea, "Sampling Type")
sampling = gui.radioButtons(self.sampling_box, self, "sampling_type",
callback=self.sampling_type_changed)
def set_sampling_type(i):
def set_sampling_type_i():
self.sampling_type = i
self.sampling_type_changed()
return set_sampling_type_i
gui.appendRadioButton(sampling, "Fixed proportion of data:")
self.sampleSizePercentageSlider = gui.hSlider(
gui.indentedBox(sampling), self,
"sampleSizePercentage",
minValue=0, maxValue=100, ticks=10, labelFormat="%d %%",
callback=set_sampling_type(self.FixedProportion))
gui.appendRadioButton(sampling, "Fixed sample size")
ibox = gui.indentedBox(sampling)
self.sampleSizeSpin = gui.spin(
ibox, self, "sampleSizeNumber", label="Instances: ",
minv=0, maxv=self._MAX_SAMPLE_SIZE,
callback=set_sampling_type(self.FixedSize),
controlWidth=90)
gui.checkBox(
ibox, self, "replacement", "Sample with replacement",
callback=set_sampling_type(self.FixedSize))
gui.appendRadioButton(sampling, "Cross validation")
form = QFormLayout(
formAlignment=Qt.AlignLeft | Qt.AlignTop,
labelAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow)
ibox = gui.indentedBox(sampling, orientation=form)
form.addRow("Number of subsets:",
gui.spin(
ibox, self, "number_of_folds", 2, 100,
addToLayout=False,
callback=self.number_of_folds_changed))
self.selected_fold_spin = gui.spin(
ibox, self, "selectedFold", 1, self.number_of_folds,
addToLayout=False, callback=self.fold_changed)
form.addRow("Unused subset:" if not self.compatibility_mode
else "Selected subset:", self.selected_fold_spin)
gui.appendRadioButton(sampling, "Bootstrap")
self.sql_box = gui.vBox(self.controlArea, "Sampling Type")
sampling = gui.radioButtons(self.sql_box, self, "sampling_type",
callback=self.sampling_type_changed)
gui.appendRadioButton(sampling, "Time:")
ibox = gui.indentedBox(sampling)
spin = gui.spin(ibox, self, "sampleSizeSqlTime", minv=1, maxv=3600,
callback=set_sampling_type(self.SqlTime))
spin.setSuffix(" sec")
gui.appendRadioButton(sampling, "Percentage")
ibox = gui.indentedBox(sampling)
spin = gui.spin(ibox, self, "sampleSizeSqlPercentage", spinType=float,
minv=0.0001, maxv=100, step=0.1, decimals=4,
callback=set_sampling_type(self.SqlProportion))
spin.setSuffix(" %")
self.sql_box.setVisible(False)
self.options_box = gui.vBox(self.controlArea, "Options", addSpaceBefore=False)
self.cb_seed = gui.checkBox(
self.options_box, self, "use_seed",
"Replicable (deterministic) sampling",
callback=self.settings_changed)
self.cb_stratify = gui.checkBox(
self.options_box, self, "stratify",
"Stratify sample (when possible)", callback=self.settings_changed)
self.cb_sql_dl = gui.checkBox(
self.options_box, self, "sql_dl", "Download data to local memory",
callback=self.settings_changed)
self.cb_sql_dl.setVisible(False)
gui.button(self.buttonsArea, self, "Sample Data",
callback=self.commit)
def sampling_type_changed(self):
self.settings_changed()
def number_of_folds_changed(self):
self.selected_fold_spin.setMaximum(self.number_of_folds)
self.sampling_type = self.CrossValidation
self.settings_changed()
def fold_changed(self):
# a separate callback - if we decide to cache indices
self.sampling_type = self.CrossValidation
def settings_changed(self):
self._update_sample_max_size()
self.indices = None
@Inputs.data
def set_data(self, dataset):
self.data = dataset
if dataset is not None:
sql = isinstance(dataset, SqlTable)
self.sampling_box.setVisible(not sql)
self.sql_box.setVisible(sql)
self.cb_seed.setVisible(not sql)
self.cb_stratify.setVisible(not sql)
self.cb_sql_dl.setVisible(sql)
if not sql:
self._update_sample_max_size()
self.updateindices()
else:
self.indices = None
self.clear_messages()
self.commit()
def _update_sample_max_size(self):
"""Limit number of instances to input size unless using replacement."""
if not self.data or self.replacement:
self.sampleSizeSpin.setMaximum(self._MAX_SAMPLE_SIZE)
else:
self.sampleSizeSpin.setMaximum(len(self.data))
def commit(self):
if self.data is None:
sample = other = None
self.sampled_instances = self.remaining_instances = None
elif isinstance(self.data, SqlTable):
other = None
if self.sampling_type == self.SqlProportion:
sample = self.data.sample_percentage(
self.sampleSizeSqlPercentage, no_cache=True)
else:
sample = self.data.sample_time(
self.sampleSizeSqlTime, no_cache=True)
if self.sql_dl:
sample.download_data()
sample = Table(sample)
else:
if self.indices is None or not self.use_seed:
self.updateindices()
if self.indices is None:
return
if self.sampling_type in (
self.FixedProportion, self.FixedSize, self.Bootstrap):
remaining, sample = self.indices
elif self.sampling_type == self.CrossValidation:
if self.compatibility_mode:
remaining, sample = self.indices[self.selectedFold - 1]
else:
sample, remaining = self.indices[self.selectedFold - 1]
sample = self.data[sample]
other = self.data[remaining]
self.sampled_instances = len(sample)
self.remaining_instances = len(other)
self.Outputs.data_sample.send(sample)
self.Outputs.remaining_data.send(other)
def updateindices(self):
self.Error.clear()
self.Warning.clear()
repl = True
data_length = len(self.data)
num_classes = len(self.data.domain.class_var.values) \
if self.data.domain.has_discrete_class else 0
size = None
if not data_length:
self.Error.no_data()
elif self.sampling_type == self.FixedSize:
size = self.sampleSizeNumber
repl = self.replacement
elif self.sampling_type == self.FixedProportion:
size = np.ceil(self.sampleSizePercentage / 100 * data_length)
repl = False
elif self.sampling_type == self.CrossValidation:
if data_length < self.number_of_folds:
self.Error.too_many_folds()
else:
assert self.sampling_type == self.Bootstrap
if not repl and size is not None and (size > data_length):
self.Error.sample_larger_than_data()
if not repl and data_length <= num_classes and self.stratify:
self.Error.not_enough_to_stratify()
if self.Error.active:
self.indices = None
return
# By the above, we can safely assume there is data
if self.sampling_type == self.FixedSize and repl and size and \
size > len(self.data):
# This should only be possible when using replacement
self.Warning.bigger_sample()
stratified = (self.stratify and
isinstance(self.data, Table) and
self.data.domain.has_discrete_class)
try:
self.indices = self.sample(data_length, size, stratified)
except ValueError as ex:
self.Warning.could_not_stratify(str(ex))
self.indices = self.sample(data_length, size, stratified=False)
def sample(self, data_length, size, stratified):
rnd = self.RandomSeed if self.use_seed else None
if self.sampling_type == self.FixedSize:
sampler = SampleRandomN(
size, stratified=stratified, replace=self.replacement,
random_state=rnd)
elif self.sampling_type == self.FixedProportion:
sampler = SampleRandomP(
self.sampleSizePercentage / 100, stratified=stratified,
random_state=rnd)
elif self.sampling_type == self.Bootstrap:
sampler = SampleBootstrap(data_length, random_state=rnd)
else:
sampler = SampleFoldIndices(
self.number_of_folds, stratified=stratified, random_state=rnd)
return sampler(self.data)
def send_report(self):
if self.sampling_type == self.FixedProportion:
tpe = f"Random sample with {self.sampleSizePercentage} % of data"
elif self.sampling_type == self.FixedSize:
if self.sampleSizeNumber == 1:
tpe = "Random data instance"
else:
tpe = f"Random sample with {self.sampleSizeNumber} data instances"
if self.replacement:
tpe += ", with replacement"
elif self.sampling_type == self.CrossValidation:
tpe = f"{self.number_of_folds}-fold cross-validation " \
f"without subset #{self.selectedFold}"
elif self.sampling_type == self.Bootstrap:
tpe = "Bootstrap"
else: # pragma: no cover
assert False
if self.stratify:
tpe += ", stratified (if possible)"
if self.use_seed:
tpe += ", deterministic"
items = [("Sampling type", tpe)]
if self.sampled_instances is not None:
items += [
("Input", f"{len(self.data)} {pl(len(self.data), 'instance')}"),
("Sample", f"{self.sampled_instances} {pl(self.sampled_instances, 'instance')}"),
("Remaining", f"{self.remaining_instances} {pl(self.remaining_instances, 'instance')}"),
]
self.report_items(items)
@classmethod
def migrate_settings(cls, settings, version):
if not version or version < 2 \
and settings["sampling_type"] == cls.CrossValidation:
settings["compatibility_mode"] = True
class SampleFoldIndices(Reprable):
def __init__(self, folds=10, stratified=False, random_state=None):
"""Samples data based on a number of folds.
Args:
folds (int): Number of folds
stratified (bool): Return stratified indices (if applicable).
random_state (Random): An initial state for replicable random
behavior
Returns:
tuple-of-arrays: A tuple of array indices one for each fold.
"""
self.folds = folds
self.stratified = stratified
self.random_state = random_state
def __call__(self, table):
if self.stratified and table.domain.has_discrete_class:
splitter = skl.StratifiedKFold(
self.folds, shuffle=True, random_state=self.random_state)
splitter.get_n_splits(table.X, table.Y)
ind = splitter.split(table.X, table.Y)
else:
splitter = skl.KFold(
self.folds, shuffle=True, random_state=self.random_state)
splitter.get_n_splits(table)
ind = splitter.split(table)
return tuple(ind)
class SampleRandomN(Reprable):
def __init__(self, n=0, stratified=False, replace=False,
random_state=None):
self.n = n
self.stratified = stratified
self.replace = replace
self.random_state = random_state
def __call__(self, table):
if self.replace:
# pylint: disable=no-member
rgen = np.random.RandomState(self.random_state)
sample = rgen.randint(0, len(table), self.n)
o = np.ones(len(table))
o[sample] = 0
others = np.nonzero(o)[0]
return others, sample
if self.n in (0, len(table)):
rgen = np.random.RandomState(self.random_state)
shuffled = np.arange(len(table))
rgen.shuffle(shuffled)
empty = np.array([], dtype=int)
if self.n == 0:
return shuffled, empty
else:
return empty, shuffled
elif self.stratified and table.domain.has_discrete_class:
test_size = max(len(table.domain.class_var.values), self.n)
splitter = skl.StratifiedShuffleSplit(
n_splits=1, test_size=test_size,
train_size=len(table) - test_size,
random_state=self.random_state)
splitter.get_n_splits(table.X, table.Y)
ind = splitter.split(table.X, table.Y)
else:
splitter = skl.ShuffleSplit(
n_splits=1, test_size=self.n, random_state=self.random_state)
splitter.get_n_splits(table)
ind = splitter.split(table)
return next(iter(ind))
class SampleRandomP(Reprable):
def __init__(self, p=0, stratified=False, random_state=None):
self.p = p
self.stratified = stratified
self.random_state = random_state
def __call__(self, table):
n = int(math.ceil(len(table) * self.p))
return SampleRandomN(n, self.stratified,
random_state=self.random_state)(table)
class SampleBootstrap(Reprable):
def __init__(self, size=0, random_state=None):
self.size = size
self.random_state = random_state
def __call__(self, table=None):
"""Bootstrap indices
Args:
table: Not used (but part of the signature)
Returns:
tuple (out_of_sample, sample) indices
"""
# pylint: disable=no-member
rgen = np.random.RandomState(self.random_state)
sample = rgen.randint(0, self.size, self.size)
sample.sort() # not needed for the code below, just for the user
insample = np.ones((self.size,), dtype=bool)
insample[sample] = False
remaining = np.flatnonzero(insample)
return remaining, sample
if __name__ == "__main__": # pragma: no cover
WidgetPreview(OWDataSampler).run(Table("iris"))
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