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from functools import partial
from types import SimpleNamespace
from typing import NamedTuple, Dict, List
import numpy as np
import scipy.sparse as sp
from AnyQt.QtCore import Qt, QSize, QAbstractListModel, QObject, \
QItemSelectionModel
from AnyQt.QtGui import QColor
from AnyQt.QtWidgets import QButtonGroup, QRadioButton, QListView
from orangewidget.utils import listview
from orangewidget.utils.itemmodels import SeparatedListDelegate, \
LabelledSeparator
from Orange.data import DiscreteVariable, ContinuousVariable, Domain, Table
from Orange.preprocess import Continuize as Continuizer
from Orange.preprocess.transformation import Identity, Indicator, Normalizer
from Orange.widgets import gui, widget
from Orange.widgets.settings import Setting
from Orange.widgets.utils.itemmodels import DomainModel
from Orange.widgets.utils.sql import check_sql_input
from Orange.widgets.utils.widgetpreview import WidgetPreview
from Orange.widgets.widget import Input, Output
class MethodDesc(NamedTuple):
id_: int
label: str # Label used for radio button
short_desc: str # Short description for list views
tooltip: str # Tooltip for radio button
supports_sparse: bool = True
DefaultKey = ""
DefaultId = 99
BackCompatClass = object()
Continuize = SimpleNamespace(
Default=DefaultId,
**{v.name: v.value for v in Continuizer.MultinomialTreatment})
DiscreteOptions: Dict[int, MethodDesc] = {
method.id_: method
for method in (
MethodDesc(
Continuize.Default, "Use preset", "preset",
"Treat the variable as defined in preset"),
MethodDesc(
Continuize.Leave, "Keep categorical", "keep as is",
"Keep the variable discrete"),
MethodDesc(
Continuize.FirstAsBase, "First value as base", "first as base",
"One indicator variable for each value except the first"),
MethodDesc(
Continuize.FrequentAsBase, "Most frequent as base", "frequent as base",
"One indicator variable for each value except the most frequent",
False),
MethodDesc(
Continuize.Indicators, "One-hot encoding", "one-hot",
"One indicator variable for each value",
False),
MethodDesc(
Continuize.RemoveMultinomial, "Remove if more than 2 values", "remove if >2",
"Remove variables with more than two values; indicator otherwise"),
MethodDesc(
Continuize.Remove, "Remove", "remove",
"Remove variable"),
MethodDesc(
Continuize.AsOrdinal, "Treat as ordinal", "as ordinal",
"Each value gets a consecutive number from 0 to number of values - 1"),
MethodDesc(
Continuize.AsNormalizedOrdinal, "Treat as normalized ordinal", "as norm. ordinal",
"Same as above, but scaled to [0, 1]")
)}
ContinuizationDefault = Continuize.FirstAsBase
Normalize = SimpleNamespace(Default=DefaultId,
Leave=0, Standardize=1, Center=2, Scale=3,
Normalize11=4, Normalize01=5)
ContinuousOptions: Dict[int, MethodDesc] = {
method.id_: method
for method in (
MethodDesc(
Normalize.Default, "Use preset", "preset",
"Treat the variable as defined in 'default setting'"),
MethodDesc(
Normalize.Leave, "Keep as it is", "no change",
"Keep the variable as it is"),
MethodDesc(
Normalize.Standardize, "Standardize to μ=0, σ²=1", "standardize",
"Subtract the mean and divide by standard deviation",
False),
MethodDesc(
Normalize.Center, "Center to μ=0", "center",
"Subtract the mean",
False),
MethodDesc(
Normalize.Scale, "Scale to σ²=1", "scale",
"Divide by standard deviation"),
MethodDesc(
Normalize.Normalize11, "Normalize to interval [-1, 1]", "to [-1, 1]",
"Linear transformation into interval [-1, 1]",
False),
MethodDesc(
Normalize.Normalize01, "Normalize to interval [0, 1]", "to [0, 1]",
"Linear transformation into interval [0, 1]",
False),
)}
NormalizationDefault = Normalize.Leave
class ContDomainModel(DomainModel):
HintRole = next(gui.OrangeUserRole)
FilterRole = next(gui.OrangeUserRole)
"""Domain model that adds description of chosen methods"""
def __init__(self, valid_type):
super().__init__(
order=(DomainModel.ATTRIBUTES,
LabelledSeparator("Meta attributes"), DomainModel.METAS,
LabelledSeparator("Targets"), DomainModel.CLASSES),
valid_types=(valid_type, ), strict_type=True)
def data(self, index, role=Qt.DisplayRole):
if role == Qt.ToolTipRole:
return None
if role == self.FilterRole:
name = super().data(index, Qt.DisplayRole)
if not isinstance(name, str):
return None
hint = index.data(self.HintRole)
if hint is None:
return name
return f"{name} {hint[0]}"
value = super().data(index, role)
if role == Qt.DisplayRole:
if isinstance(value, LabelledSeparator):
return None
return value, *(index.data(self.HintRole) or ("", False))
return value
class DefaultContModel(QAbstractListModel):
"""A model used for showing "Default settings" above the list view"""
icon = None
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
if DefaultContModel.icon is None:
DefaultContModel.icon = gui.createAttributePixmap(
"★", QColor(0, 0, 0, 0), Qt.black)
self.method = ""
@staticmethod
def rowCount(parent):
return 0 if parent.isValid() else 1
@staticmethod
def columnCount(parent):
return 0 if parent.isValid() else 1
def data(self, _, role=Qt.DisplayRole):
if role == Qt.DisplayRole:
return f"Preset: {self.method}"
elif role == Qt.DecorationRole:
return self.icon
elif role == Qt.ToolTipRole:
return "Default for variables without specific settings"
return None
def setMethod(self, method):
self.method = method
self.dataChanged.emit(self.index(0, 0), self.index(0, 0))
class ListViewSearch(listview.ListViewSearch):
"""
A list view with two components shown above it:
- a listview containing a single item representing default settings
- a filter for search
The class is based on listview.ListViewSearch and needs to have the same
name in order to override its private method __layout.
Inherited __init__ calls __layout, so `default_view` must be constructed
there. Construction before calling super().__init__ doesn't work because
PyQt does not allow it.
"""
class Delegate(SeparatedListDelegate):
"""
A delegate that shows items (variables) with specific settings in bold
"""
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._default_hints = False
def initStyleOption(self, option, index):
super().initStyleOption(option, index)
hint = index.data(ContDomainModel.HintRole)
option.font.setBold(hint is not None and hint[1])
def set_default_hints(self, show):
self._default_hints = show
def displayText(self, value, _):
if value is None:
return None
name, hint, nondefault = value
if self._default_hints or nondefault:
name += f": {hint}"
return name
def __init__(self, *args, **kwargs):
self.default_view = None
super().__init__(preferred_size=QSize(350, -1), *args, **kwargs)
self.setItemDelegate(self.Delegate(self))
self.force_hints = False
def select_default(self):
"""Select the item representing default settings"""
self.default_view.selectionModel().select(
self.default_view.model().index(0),
QItemSelectionModel.Select)
def set_default_method(self, method):
self.default_view.model().setMethod(method)
# pylint: disable=unused-private-member
def __layout(self):
if self.default_view is None: # __layout was called from __init__
view = self.default_view = QListView(self)
view.setModel(DefaultContModel())
self.filterProxyModel().setFilterRole(ContDomainModel.FilterRole)
view.verticalScrollBar().setDisabled(True)
view.horizontalScrollBar().setDisabled(True)
view.setHorizontalScrollBarPolicy(
Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
view.setVerticalScrollBarPolicy(
Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
font = view.font()
font.setBold(True)
view.setFont(font)
else:
view = self.default_view
# Put the list view with default on top
margins = self.viewportMargins()
def_height = view.sizeHintForRow(0) + 2 * view.spacing() + 2
view.setGeometry(0, 0, self.geometry().width(), def_height)
view.setFixedHeight(def_height)
# Then search
search = self.__search
src_height = search.sizeHint().height()
size = self.size()
search.setGeometry(0, def_height + 2, size.width(), src_height)
# Then the real list view
margins.setTop(def_height + 2 + src_height)
self.setViewportMargins(margins)
def event(self, ev):
if ev.type() == ev.ToolTip:
self.itemDelegate().set_default_hints(True)
self.viewport().update()
return True
return super().event(ev)
def leaveEvent(self, _):
self.itemDelegate().set_default_hints(False)
self.viewport().update()
class OWContinuize(widget.OWWidget):
# Many false positives for `hints`; pylint ignores type annotations
# pylint: disable=unsubscriptable-object,unsupported-assignment-operation
# pylint: disable=unsupported-membership-test, unsupported-delete-operation
name = "Continuize"
description = ("Transform categorical attributes into numeric and, " +
"optionally, scale numeric values.")
icon = "icons/Continuize.svg"
category = "Transform"
keywords = "continuize, encode, dummy, numeric, one-hot, binary, treatment, contrast"
priority = 2120
class Inputs:
data = Input("Data", Table)
class Outputs:
data = Output("Data", Table)
class Error(widget.OWWidget.Error):
unsupported_sparse = \
widget.Msg("Some chosen methods do not support sparse data: {}")
want_control_area = False
settings_version = 3
disc_var_hints: Dict[str, int] = Setting(
{DefaultKey: ContinuizationDefault}, schema_only=True)
cont_var_hints: Dict[str, int] = Setting(
{DefaultKey: NormalizationDefault}, schema_only=True)
autosend = Setting(True)
def __init__(self):
super().__init__()
self.data = None
self._var_cache = {}
def create(title, vartype, methods):
hbox = gui.hBox(box, title)
view = ListViewSearch(
selectionMode=ListViewSearch.ExtendedSelection,
uniformItemSizes=True)
view.setModel(ContDomainModel(vartype))
view.selectionModel().selectionChanged.connect(
lambda: self._on_var_selection_changed(view))
view.default_view.selectionModel().selectionChanged.connect(
lambda selected: self._on_default_selected(view, selected))
hbox.layout().addWidget(view)
bbox = gui.vBox(hbox)
bgroup = QButtonGroup(self)
bgroup.idClicked.connect(self._on_radio_clicked)
for desc in methods.values():
button = QRadioButton(desc.label)
button.setToolTip(desc.tooltip)
bgroup.addButton(button, desc.id_)
bbox.layout().addWidget(button)
bbox.layout().addStretch(1)
return hbox, view, bbox, bgroup
box = gui.vBox(self.mainArea, True, spacing=8)
self.disc_box, self.disc_view, self.disc_radios, self.disc_group = \
create("Categorical Variables", DiscreteVariable, DiscreteOptions)
self.disc_view.set_default_method(
DiscreteOptions[self.disc_var_hints[DefaultKey]].short_desc)
self.disc_view.select_default()
self.cont_box, self.cont_view, self.cont_radios, self.cont_group = \
create("Numeric Variables", ContinuousVariable, ContinuousOptions)
self.cont_view.set_default_method(
ContinuousOptions[self.cont_var_hints[DefaultKey]].short_desc)
self.cont_view.select_default()
boxes = (self.disc_radios, self.cont_radios)
width = max(box.sizeHint().width() for box in boxes)
for box in boxes:
box.setFixedWidth(width)
box = gui.hBox(self.mainArea)
gui.button(
box, self, "Reset All", callback=self._on_reset_hints,
autoDefault=False)
gui.rubber(box)
gui.auto_apply(box, self, "autosend")
def _on_var_selection_changed(self, view):
if not view.selectionModel().selectedIndexes():
# Prevent infinite recursion (with _on_default_selected)
return
view.default_view.selectionModel().clearSelection()
self._update_radios(view)
def _on_default_selected(self, view, selected):
if not selected:
# Prevent infinite recursion (with _var_selection_selected)
return
view.selectionModel().clearSelection()
self._update_radios(view)
def selected_vars(self, view) -> List[str]:
"""
Return selected variables
If 'Default settings' are selected, this returns DefaultKey
"""
model = view.model()
return [model[index.row()]
for index in view.selectionModel().selectedRows()]
def _update_radios(self, view):
if view is self.disc_view:
group, hints = self.disc_group, self.disc_var_hints
else:
group, hints = self.cont_group, self.cont_var_hints
selvars = self.selected_vars(view)
if not selvars:
self._check_button(group, hints[DefaultKey], True)
self._set_radio_enabled(group, DefaultId, False)
return
self._set_radio_enabled(group, DefaultId, True)
options = {hints.get(var.name, self.default_for_var(var))
for var in selvars}
if len(options) == 1:
self._check_button(group, options.pop(), True)
else:
self._uncheck_all_buttons(group)
@staticmethod
def _uncheck_all_buttons(group: QButtonGroup):
button = group.checkedButton()
if button is not None:
group.setExclusive(False)
button.setChecked(False)
group.setExclusive(True)
def _set_radio_enabled(
self, group: QButtonGroup, method_id: int, value: bool):
if group.button(method_id).isChecked() and not value:
self._uncheck_all_buttons(group)
group.button(method_id).setEnabled(value)
@staticmethod
def _check_button(group: QButtonGroup, method_id: int, checked: bool):
group.button(method_id).setChecked(checked)
def _on_radio_clicked(self, method_id: int):
if QObject().sender() is self.disc_group:
view, hints, methods = \
self.disc_view, self.disc_var_hints, DiscreteOptions
leave_id = Continuize.Leave
else:
view, hints, methods = \
self.cont_view, self.cont_var_hints, ContinuousOptions
leave_id = Normalize.Leave
selvars = self.selected_vars(view)
if not selvars:
hints[DefaultKey] = method_id
view.set_default_method(methods[method_id].short_desc)
else:
keys = [var.name for var in selvars]
indexes = view.selectionModel().selectedIndexes()
model = view.model()
# These two keys may delete values from dict, hence we must loop
if method_id in (DefaultId, leave_id):
for key in keys:
# Attributes do not store the hint if it equals Default;
# metas and targets do not store it if it is Leave
if method_id == (DefaultId if self.is_attr(key) else leave_id):
if key in hints:
del hints[key]
else:
hints[key] = method_id
else:
hints.update(dict.fromkeys(keys, method_id))
desc = methods[method_id].short_desc
for index, var in zip(indexes, selvars):
show = method_id != self.default_for_var(var)
model.setData(index, (desc, show), model.HintRole)
self.commit.deferred()
@Inputs.data
@check_sql_input
def set_data(self, data):
self.data = data
self._var_cache.clear()
domain = data.domain if data else None
self.disc_view.model().set_domain(domain)
self.cont_view.model().set_domain(domain)
if data:
# Clean up hints only when receiving new data, not on disconnection
self._set_hints()
self.commit.now()
def _set_hints(self):
assert self.data
# Backward compatibility for settings < 3
class_treatment = self.disc_var_hints.get(BackCompatClass, None)
if class_treatment is not None \
and self.data.domain.class_var is not None:
self.disc_var_hints[self.data.domain.class_var.name] \
= class_treatment
for hints, model, options in (
(self.cont_var_hints, self.cont_view.model(), ContinuousOptions),
(self.disc_var_hints, self.disc_view.model(), DiscreteOptions)):
filtered = {DefaultKey: hints[DefaultKey]}
for i, var in enumerate(model):
if isinstance(var, LabelledSeparator):
continue
default = self.default_for_var(var)
method_id = hints.get(var.name, default)
nondefault = method_id != default
if nondefault:
filtered[var.name] = method_id
model.setData(
model.index(i, 0),
(options[method_id].short_desc, nondefault),
model.HintRole)
hints.clear()
hints.update(filtered)
def _on_reset_hints(self):
if not self.data:
return
self.cont_var_hints.clear()
self.disc_var_hints.clear()
self.disc_var_hints[DefaultKey] = ContinuizationDefault
self.cont_var_hints[DefaultKey] = NormalizationDefault
self._set_hints()
self.cont_view.set_default_method(
ContinuousOptions[ContinuizationDefault].short_desc)
self.disc_view.set_default_method(
ContinuousOptions[NormalizationDefault].short_desc)
@gui.deferred
def commit(self):
self.Outputs.data.send(self._prepare_output())
def _prepare_output(self):
self.Error.unsupported_sparse.clear()
if not self.data:
return None
if unsupp_sparse := self._unsupported_sparse():
if len(unsupp_sparse) == 1:
self.Error.unsupported_sparse(unsupp_sparse[0])
else:
self.Error.unsupported_sparse("\n" + ", ".join(unsupp_sparse))
return None
domain = self.data.domain
attrs = self._create_vars(domain.attributes)
class_vars = self._create_vars(domain.class_vars)
metas = self._create_vars(domain.metas)
return self.data.transform(Domain(attrs, class_vars, metas))
def _unsupported_sparse(self):
# time is not continuous, pylint: disable=unidiomatic-typecheck
domain = self.data.domain
disc = set()
cont = set()
# At the time of writing, self.data.Y cannot be sparse (setter for
# `Y` converts it to dense, as done in
# https://github.com/biolab/orange3/commit/a18f38059caf37f3b329d6ad688189561959bb24)
# Including it here doesn't hurt, though.
for part, attrs in ((self.data.X, domain.attributes),
(self.data.Y, domain.class_vars),
(self.data.metas, domain.metas)):
if sp.issparse(part):
disc |= {self._hint_for_var(var)
for var in attrs
if var.is_discrete}
cont |= {self._hint_for_var(var)
for var in attrs
if type(var) is ContinuousVariable}
disc &= {method.id_
for method in DiscreteOptions.values()
if not method.supports_sparse}
cont &= {method.id_
for method in ContinuousOptions.values()
if not method.supports_sparse}
# Retrieve them from DiscreteOptions/ContinuousOptions to keep the order
return [method.label
for methods, problems in ((DiscreteOptions, disc),
(ContinuousOptions, cont))
for method in methods.values() if method.id_ in problems]
def _create_vars(self, part):
# time is not continuous, pylint: disable=unidiomatic-typecheck
return sum(
(self._continuized_vars(var) if var.is_discrete
else self._scaled_vars(var) if type(var) is ContinuousVariable
else [var]
for var in part),
start=[])
def _get(self, var, stat):
def most_frequent(col):
col = col[np.isfinite(col)].astype(int)
counts = np.bincount(col, minlength=len(var.values))
return np.argmax(counts)
funcs = {"min": np.nanmin, "max": np.nanmax,
"mean": np.nanmean, "std": np.nanstd,
"major": most_frequent}
name = var.name
cache = self._var_cache.setdefault(name, {})
if stat not in cache:
cache[stat] = funcs[stat](self.data.get_column(var))
return cache[stat]
def is_attr(self, var):
domain = self.data.domain
return 0 <= domain.index(var) < len(domain.attributes)
def default_for_var(self, var):
if self.is_attr(var):
return DefaultId
return Continuize.Leave if var.is_discrete else Normalize.Leave
def _hint_for_var(self, var):
if var.is_discrete:
hints, leave_id = self.disc_var_hints, Continuize.Leave
else:
hints, leave_id = self.cont_var_hints, Normalize.Leave
# Default for attributes is given by "default"
if self.is_attr(var):
return hints.get(var.name, hints[DefaultKey])
# For metas and targets, default is Leave
# If user changes it to "Default", default is used
hint = hints.get(var.name, leave_id)
if hint == DefaultId:
hint = hints[DefaultKey]
return hint
def _scaled_vars(self, var):
hint = self._hint_for_var(var)
if hint == Normalize.Leave:
return [var]
get = partial(self._get, var)
if hint == Normalize.Standardize:
off, scale = get("mean"), 1 / (get("std") or 1)
elif hint == Normalize.Center:
off, scale = get("mean"), 1
elif hint == Normalize.Scale:
off, scale = 0, 1 / (get("std") or 1)
else:
assert hint in (Normalize.Normalize11, Normalize.Normalize01), f"hint={hint}?!"
min_, max_ = get("min"), get("max")
span = (max_ - min_) or 1
if hint == Normalize.Normalize11:
off, scale = (min_ + max_) / 2, 2 / span
else:
off, scale = min_, 1 / span
return [ContinuousVariable(
var.name,
compute_value=Normalizer(var, off, scale))]
def _continuized_vars(self, var, hint=None):
if hint is None:
hint = self._hint_for_var(var)
# Single variable
if hint == Continuize.Leave:
return [var]
if hint == Continuize.Remove:
return []
if hint == Continuize.RemoveMultinomial and len(var.values) <= 2 or \
hint == Continuize.AsOrdinal:
return [ContinuousVariable(var.name,
compute_value=Identity(var))]
if hint == Continuize.RemoveMultinomial:
assert len(var.values) > 2
return []
if hint == Continuize.AsOrdinal:
return [ContinuousVariable(var.name,
compute_value=Identity(var))]
if hint == Continuize.AsNormalizedOrdinal:
scale = 1 / (len(var.values) - 1 or 1)
return [ContinuousVariable(var.name,
compute_value=Normalizer(var, 0, scale))]
# Multiple dummy variables
if hint == Continuize.FirstAsBase:
base = 0
elif hint == Continuize.FrequentAsBase:
base = self._get(var, "major")
elif hint == Continuize.Indicators:
base = None
else:
assert False, f"hint={hint}?!"
return [
ContinuousVariable(f"{var.name}={value}",
compute_value=Indicator(var, value=i))
for i, value in enumerate(var.values)
if i != base
]
def send_report(self):
if not self.data:
return
single_disc = len(self.disc_view.model()) > 0 \
and len(self.disc_var_hints) == 1 \
and DiscreteOptions[self.disc_var_hints[DefaultKey]].label.lower()
single_cont = len(self.cont_view.model()) > 0 \
and len(self.cont_var_hints) == 1 \
and ContinuousOptions[self.cont_var_hints[DefaultKey]].label.lower()
if single_disc and single_cont:
self.report_items(
(("Categorical variables", single_disc),
("Numeric variables", single_cont))
)
else:
if single_disc:
self.report_paragraph("Categorical variables", single_disc)
elif len(self.disc_view.model()) > 0:
self.report_items(
"Categorical variables",
[("Preset" if name == DefaultKey else name,
DiscreteOptions[id_].label.lower())
for name, id_ in self.disc_var_hints.items()])
if single_cont:
self.report_paragraph("Numeric variables", single_cont)
elif len(self.cont_view.model()) > 0:
self.report_items(
"Numeric variables",
[("Preset" if name == DefaultKey else name,
ContinuousOptions[id_].label.lower())
for name, id_ in self.cont_var_hints.items()])
self.report_paragraph("Unlisted",
"Any unlisted attributes default to preset option, and "
"unlisted meta attributes and target variables are kept "
"as they are")
@classmethod
def migrate_settings(cls, settings, version):
if version < 2:
cont_treat = settings.pop("continuous_treatment", 0)
zero_based = settings.pop("zero_based", True)
if cont_treat == 1:
if zero_based:
settings["continuous_treatment"] = Normalize.Normalize01
else:
settings["continuous_treatment"] = Normalize.Normalize11
elif cont_treat == 2:
settings["continuous_treatment"] = Normalize.Standardize
if version < 3:
settings["cont_var_hints"] = \
{DefaultKey:
settings.pop("continuous_treatment", Normalize.Leave)}
# DISC OPS: Default=99, Indicators=1, FirstAsBase=2, FrequentAsBase=3, Remove=4,
# RemoveMultinomial=5, ReportError=6, AsOrdinal=7, AsNormalizedOrdinal=8, Leave=9
# OLD ORDER: [FirstAsBase, FrequentAsBase, Indicators, RemoveMultinomial, Remove,
# AsOrdinal, AsNormalizedOrdinal]
old_to_new = [2, 3, 1, 5, 4, 7, 8]
settings["disc_var_hints"] = \
{DefaultKey:
old_to_new[settings.pop("multinomial_treatment", 0)]}
# OLD ORDER: [Leave, AsOrdinal, AsNormalizedOrdinal, Indicators]
old_to_new = [9, 7, 8, 1]
class_treatment = old_to_new[settings.pop("class_treatment", 0)]
if class_treatment != Continuize.Leave:
settings["disc_var_hints"][BackCompatClass] = class_treatment
# Backward compatibility for unpickling settings
OWContinuize.Normalize = Normalize
if __name__ == "__main__": # pragma: no cover
WidgetPreview(OWContinuize).run(Table("heart_disease"))
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