from collections import defaultdict, namedtuple
from xml.sax.saxutils import escape

import numpy as np
import scipy.sparse as sp

from AnyQt.QtCore import Qt, QRectF, pyqtSignal as Signal, QObject, QThread, \
    pyqtSlot as Slot
from AnyQt.QtGui import QTransform, QPen, QBrush, QColor, QPainter, \
    QPainterPath, QKeyEvent
from AnyQt.QtWidgets import \
    QGraphicsView, QGraphicsScene, \
    QGraphicsItem, QGraphicsRectItem, QGraphicsItemGroup, QSizePolicy, \
    QGraphicsPathItem

from Orange.data import Table, Domain
from Orange.preprocess import decimal_binnings, time_binnings
from Orange.projection.som import SOM

from Orange.widgets import gui
from Orange.widgets.widget import OWWidget, Msg, Input, Output
from Orange.widgets.settings import \
    DomainContextHandler, ContextSetting, Setting
from Orange.widgets.utils.itemmodels import DomainModel
from Orange.widgets.utils.widgetpreview import WidgetPreview
from Orange.widgets.utils.state_summary import format_summary_details
from Orange.widgets.utils.annotated_data import \
    create_annotated_table, create_groups_table, ANNOTATED_DATA_SIGNAL_NAME
from Orange.widgets.utils.colorpalettes import \
    BinnedContinuousPalette, LimitedDiscretePalette
from Orange.widgets.visualize.utils import CanvasRectangle, CanvasText
from Orange.widgets.visualize.utils.plotutils import wrap_legend_items


sqrt3_2 = np.sqrt(3) / 2


class SomView(QGraphicsView):
    SelectionSet, SelectionNewGroup, SelectionAddToGroup, SelectionRemove \
        = range(4)
    selection_changed = Signal(np.ndarray, int)
    selection_moved = Signal(QKeyEvent)
    selection_mark_changed = Signal(np.ndarray)

    def __init__(self, scene):
        super().__init__(scene)
        self.__button_down_pos = None
        self.size_x = self.size_y = 1
        self.hexagonal = True

    def set_dimensions(self, size_x, size_y, hexagonal):
        self.size_x = size_x
        self.size_y = size_y
        self.hexagonal = hexagonal

    def _get_marked_cells(self, event):
        x0, y0 = self.__button_down_pos.x(), self.__button_down_pos.y()
        pos = self.mapToScene(event.pos())
        x1, y1 = pos.x(), pos.y()
        x0, x1 = sorted((x0, x1))
        y0, y1 = sorted((y0, y1))
        selection = np.zeros((self.size_x, self.size_y), dtype=bool)
        if self.hexagonal:
            y0 = max(0, int(y0 / sqrt3_2 + 0.5))
            y1 = min(self.size_y, int(np.ceil(y1 / sqrt3_2 + 0.5)))
            for y in range(y0, y1):
                if x1 < 0:
                    continue
                x0_ = max(0, int(x0 + 0.5 - (y % 2) / 2))
                x1_ = min(self.size_x - y % 2,
                          int(np.ceil(x1 + 0.5 - (y % 2) / 2)))
                selection[x0_:x1_, y] = True
        elif not(x1 < -0.5 or x0 > self.size_x - 0.5
                 or y1 < -0.5 or y0 > self.size_y - 0.5):

            def roundclip(z, zmax):
                return int(np.clip(np.round(z), 0, zmax - 1))\

            x0 = roundclip(x0, self.size_x)
            y0 = roundclip(y0, self.size_y)
            x1 = roundclip(x1, self.size_x)
            y1 = roundclip(y1, self.size_y)
            selection[x0:x1 + 1, y0:y1 + 1] = True

        return selection

    def mousePressEvent(self, event):
        if event.button() != Qt.LeftButton:
            return

        self.__button_down_pos = self.mapToScene(event.pos())
        event.accept()

    def mouseMoveEvent(self, event):
        if event.buttons() != Qt.LeftButton:
            return

        self.selection_mark_changed.emit(self._get_marked_cells(event))
        event.accept()

    def mouseReleaseEvent(self, event):
        if event.button() != Qt.LeftButton:
            return

        if event.modifiers() & Qt.ShiftModifier:
            if event.modifiers() & Qt.ControlModifier:
                action = self.SelectionAddToGroup
            else:
                action = self.SelectionNewGroup
        elif event.modifiers() & Qt.AltModifier:
            action = self.SelectionRemove
        else:
            action = self.SelectionSet
        selection = self._get_marked_cells(event)
        self.selection_changed.emit(selection, action)
        event.accept()

    def keyPressEvent(self, event: QKeyEvent):
        if event.key() in (Qt.Key_Up, Qt.Key_Down, Qt.Key_Left, Qt.Key_Right):
            self.selection_moved.emit(event)
        else:
            super().keyPressEvent(event)


class PieChart(QGraphicsItem):
    def __init__(self, dist, r, colors):
        super().__init__()
        self.dist = dist
        self.r = r
        self.colors = colors

    def boundingRect(self):
        return QRectF(- self.r, - self.r, 2 * self.r, 2 * self.r)

    def paint(self, painter, _option, _index):
        painter.save()
        start_angle = 0
        pen = QPen(QBrush(Qt.black), 2)
        pen.setCosmetic(True)
        painter.setPen(pen)
        painter.drawEllipse(self.boundingRect())
        for angle, color in zip(self.dist * 16 * 360, self.colors):
            if angle == 0:
                continue
            painter.setBrush(QBrush(color))
            painter.setPen(Qt.NoPen)
            painter.drawPie(self.boundingRect(), int(start_angle), int(angle))
            start_angle += angle
        painter.restore()


class ColoredCircle(QGraphicsItem):
    def __init__(self, r, color, proportion):
        super().__init__()
        self.r = r
        self.color = color
        self.proportion = proportion

    def boundingRect(self):
        return QRectF(-self.r, -self.r, 2 * self.r, 2 * self.r)

    def paint(self, painter, _option, _index):
        painter.save()
        pen = QPen(QBrush(self.color), 2)
        pen.setCosmetic(True)
        painter.setPen(pen)
        painter.setBrush(QBrush(self.color.lighter(200 - 80 * self.proportion)))
        painter.drawEllipse(self.boundingRect())
        painter.restore()


N_ITERATIONS = 200


class OWSOM(OWWidget):
    name = "Self-Organizing Map"
    description = "Computation of self-organizing map."
    icon = "icons/SOM.svg"
    keywords = ["SOM"]

    class Inputs:
        data = Input("Data", Table)

    class Outputs:
        selected_data = Output("Selected Data", Table, default=True)
        annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Table)

    settingsHandler = DomainContextHandler()
    auto_dimension = Setting(True)
    size_x = Setting(10)
    size_y = Setting(10)
    hexagonal = Setting(1)
    initialization = Setting(0)

    attr_color = ContextSetting(None)
    size_by_instances = Setting(True)
    pie_charts = Setting(False)
    selection = Setting(None, schema_only=True)

    graph_name = "view"

    _grid_pen = QPen(QBrush(QColor(224, 224, 224)), 2)
    _grid_pen.setCosmetic(True)

    OptControls = namedtuple(
        "OptControls",
        ("shape", "auto_dim", "spin_x", "spin_y", "initialization", "start")
    )

    class Warning(OWWidget.Warning):
        ignoring_disc_variables = Msg("SOM ignores categorical variables.")
        missing_colors = \
            Msg("Some data instances have undefined value of '{}'.")
        missing_values = \
            Msg("{} data instance{} with undefined value(s) {} not shown.")
        single_attribute = Msg("Data contains a single numeric column.")

    class Error(OWWidget.Error):
        no_numeric_variables = Msg("Data contains no numeric columns.")
        no_defined_rows = Msg("All rows contain at least one undefined value.")

    def __init__(self):
        super().__init__()
        self.__pending_selection = self.selection
        self._optimizer = None
        self._optimizer_thread = None
        self.stop_optimization = False

        self.data = self.cont_x = None
        self.cells = self.member_data = None
        self.selection = None
        self.colors = self.thresholds = self.bin_labels = None

        self._set_input_summary(None)
        self._set_output_summary(None)

        box = gui.vBox(self.controlArea, box="SOM")
        shape = gui.comboBox(
            box, self, "", items=("Hexagonal grid", "Square grid"))
        shape.setCurrentIndex(1 - self.hexagonal)

        box2 = gui.indentedBox(box, 10)
        auto_dim = gui.checkBox(
            box2, self, "auto_dimension", "Set dimensions automatically",
            callback=self.on_auto_dimension_changed)
        self.manual_box = box3 = gui.hBox(box2)
        spinargs = dict(
            value="", widget=box3, master=self, minv=5, maxv=100, step=5,
            alignment=Qt.AlignRight)
        spin_x = gui.spin(**spinargs)
        spin_x.setValue(self.size_x)
        gui.widgetLabel(box3, "×")
        spin_y = gui.spin(**spinargs)
        spin_y.setValue(self.size_y)
        gui.rubber(box3)
        self.manual_box.setEnabled(not self.auto_dimension)

        initialization = gui.comboBox(
            box, self, "initialization",
            items=("Initialize with PCA", "Random initialization",
                   "Replicable random"))

        start = gui.button(
            box, self, "Restart", callback=self.restart_som_pressed,
            sizePolicy=(QSizePolicy.MinimumExpanding, QSizePolicy.Fixed))

        self.opt_controls = self.OptControls(
            shape, auto_dim, spin_x, spin_y, initialization, start)

        box = gui.vBox(self.controlArea, "Color")
        gui.comboBox(
            box, self, "attr_color", searchable=True,
            callback=self.on_attr_color_change,
            model=DomainModel(placeholder="(Same color)",
                              valid_types=DomainModel.PRIMITIVE))
        gui.checkBox(
            box, self, "pie_charts", label="Show pie charts",
            callback=self.on_pie_chart_change)
        gui.checkBox(
            box, self, "size_by_instances", label="Size by number of instances",
            callback=self.on_attr_size_change)

        gui.rubber(self.controlArea)

        self.scene = QGraphicsScene(self)

        self.view = SomView(self.scene)
        self.view.setMinimumWidth(400)
        self.view.setMinimumHeight(400)
        self.view.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
        self.view.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
        self.view.setRenderHint(QPainter.Antialiasing)
        self.view.selection_changed.connect(self.on_selection_change)
        self.view.selection_moved.connect(self.on_selection_move)
        self.view.selection_mark_changed.connect(self.on_selection_mark_change)
        self.mainArea.layout().addWidget(self.view)

        self.elements = None
        self.grid = None
        self.grid_cells = None
        self.legend = None

    @Inputs.data
    def set_data(self, data):
        def prepare_data():
            if len(cont_attrs) < len(attrs):
                self.Warning.ignoring_disc_variables()
            if len(cont_attrs) == 1:
                self.Warning.single_attribute()
            x = Table.from_table(Domain(cont_attrs), data).X
            if sp.issparse(x):
                self.data = data
                self.cont_x = x.tocsr()
            else:
                mask = np.all(np.isfinite(x), axis=1)
                if not np.any(mask):
                    self.Error.no_defined_rows()
                else:
                    if np.all(mask):
                        self.data = data
                        self.cont_x = x.copy()
                    else:
                        self.data = data[mask]
                        self.cont_x = x[mask]
                    self.cont_x -= np.min(self.cont_x, axis=0)[None, :]
                    sums = np.sum(self.cont_x, axis=0)[None, :]
                    sums[sums == 0] = 1
                    self.cont_x /= sums

        def set_warnings():
            missing = len(data) - len(self.data)
            if missing == 1:
                self.Warning.missing_values(1, "", "is")
            elif missing > 1:
                self.Warning.missing_values(missing, "s", "are")

        self.stop_optimization_and_wait()

        self.closeContext()
        self.clear()
        self.Error.clear()
        self.Warning.clear()

        if data is not None:
            attrs = data.domain.attributes
            cont_attrs = [var for var in attrs if var.is_continuous]
            if not cont_attrs:
                self.Error.no_numeric_variables()
            else:
                prepare_data()

        if self.data is not None:
            self.controls.attr_color.model().set_domain(data.domain)
            self.attr_color = data.domain.class_var
            set_warnings()

        self.openContext(self.data)
        self.set_color_bins()
        self.create_legend()
        self.recompute_dimensions()
        self._set_input_summary(data)
        self.start_som()

    def _set_input_summary(self, data):
        summary = len(data) if data else self.info.NoInput
        details = format_summary_details(data) if data else ""
        self.info.set_input_summary(summary, details)

    def _set_output_summary(self, output):
        summary = len(output) if output else self.info.NoOutput
        details = format_summary_details(output) if output else ""
        self.info.set_output_summary(summary, details)

    def clear(self):
        self.data = self.cont_x = None
        self.cells = self.member_data = None
        self.attr_color = None
        self.colors = self.thresholds = self.bin_labels = None
        if self.elements is not None:
            self.scene.removeItem(self.elements)
            self.elements = None
        self.clear_selection()
        self.controls.attr_color.model().set_domain(None)
        self.Warning.clear()
        self.Error.clear()

    def recompute_dimensions(self):
        if not self.auto_dimension or self.cont_x is None:
            return
        dim = max(5, int(np.ceil(np.sqrt(5 * np.sqrt(self.cont_x.shape[0])))))
        self.opt_controls.spin_x.setValue(dim)
        self.opt_controls.spin_y.setValue(dim)

    def on_auto_dimension_changed(self):
        self.manual_box.setEnabled(not self.auto_dimension)
        if self.auto_dimension:
            self.recompute_dimensions()
        else:
            spin_x = self.opt_controls.spin_x
            spin_y = self.opt_controls.spin_y
            dimx = int(5 * np.round(spin_x.value() / 5))
            dimy = int(5 * np.round(spin_y.value() / 5))
            spin_x.setValue(dimx)
            spin_y.setValue(dimy)

    def on_attr_color_change(self):
        self.controls.pie_charts.setEnabled(self.attr_color is not None)
        self.set_color_bins()
        self.create_legend()
        self.rescale()
        self._redraw()

    def on_attr_size_change(self):
        self._redraw()

    def on_pie_chart_change(self):
        self._redraw()

    def clear_selection(self):
        self.selection = None
        self.redraw_selection()

    def on_selection_change(self, selection, action=SomView.SelectionSet):
        if self.data is None:  # clicks on empty canvas
            return
        if self.selection is None:
            self.selection = np.zeros(self.grid_cells.T.shape, dtype=np.int16)
        if action == SomView.SelectionSet:
            self.selection[:] = 0
            self.selection[selection] = 1
        elif action == SomView.SelectionAddToGroup:
            self.selection[selection] = max(1, np.max(self.selection))
        elif action == SomView.SelectionNewGroup:
            self.selection[selection] = 1 + np.max(self.selection)
        elif action & SomView.SelectionRemove:
            self.selection[selection] = 0
        self.redraw_selection()
        self.update_output()

    def on_selection_move(self, event: QKeyEvent):
        if self.selection is None or not np.any(self.selection):
            if event.key() in (Qt.Key_Right, Qt.Key_Down):
                x = y = 0
            else:
                x = self.size_x - 1
                y = self.size_y - 1
        else:
            x, y = np.nonzero(self.selection)
            if len(x) > 1:
                return
            if event.key() == Qt.Key_Up and y > 0:
                y -= 1
            if event.key() == Qt.Key_Down and y < self.size_y - 1:
                y += 1
            if event.key() == Qt.Key_Left and x:
                x -= 1
            if event.key() == Qt.Key_Right and x < self.size_x - 1:
                x += 1
            x -= self.hexagonal and x == self.size_x - 1 and y % 2

        if self.selection is not None and self.selection[x, y]:
            return
        selection = np.zeros(self.grid_cells.shape, dtype=bool)
        selection[x, y] = True
        self.on_selection_change(selection)

    def on_selection_mark_change(self, marks):
        self.redraw_selection(marks=marks)

    def redraw_selection(self, marks=None):
        if self.grid_cells is None:
            return

        sel_pen = QPen(QBrush(QColor(128, 128, 128)), 2)
        sel_pen.setCosmetic(True)
        mark_pen = QPen(QBrush(QColor(128, 128, 128)), 4)
        mark_pen.setCosmetic(True)
        pens = [self._grid_pen, sel_pen]

        mark_brush = QBrush(QColor(224, 255, 255))
        sels = self.selection is not None and np.max(self.selection)
        palette = LimitedDiscretePalette(number_of_colors=sels + 1)
        brushes = [QBrush(Qt.NoBrush)] + \
                  [QBrush(palette[i].lighter(165)) for i in range(sels)]

        for y in range(self.size_y):
            for x in range(self.size_x - (y % 2) * self.hexagonal):
                cell = self.grid_cells[y, x]
                marked = marks is not None and marks[x, y]
                sel_group = self.selection is not None and self.selection[x, y]
                if marked:
                    cell.setBrush(mark_brush)
                    cell.setPen(mark_pen)
                else:
                    cell.setBrush(brushes[sel_group])
                    cell.setPen(pens[bool(sel_group)])
                cell.setZValue(marked or sel_group)

    def restart_som_pressed(self):
        if self._optimizer_thread is not None:
            self.stop_optimization = True
            self._optimizer.stop_optimization = True
        else:
            self.start_som()

    def start_som(self):
        self.read_controls()
        self.update_layout()
        self.clear_selection()
        if self.cont_x is not None:
            self.enable_controls(False)
            self._recompute_som()
        else:
            self.update_output()

    def read_controls(self):
        c = self.opt_controls
        self.hexagonal = c.shape.currentIndex() == 0
        self.size_x = c.spin_x.value()
        self.size_y = c.spin_y.value()

    def enable_controls(self, enable):
        c = self.opt_controls
        c.shape.setEnabled(enable)
        c.auto_dim.setEnabled(enable)
        c.start.setText("Start" if enable else "Stop")

    def update_layout(self):
        self.set_legend_pos()
        if self.elements:  # Prevent having redrawn grid but with old elements
            self.scene.removeItem(self.elements)
            self.elements = None
        self.redraw_grid()
        self.rescale()

    def _redraw(self):
        self.Warning.missing_colors.clear()
        if self.elements:
            self.scene.removeItem(self.elements)
            self.elements = None
        self.view.set_dimensions(self.size_x, self.size_y, self.hexagonal)

        if self.cells is None:
            return
        sizes = self.cells[:, :, 1] - self.cells[:, :, 0]
        sizes = sizes.astype(float)
        if not self.size_by_instances:
            sizes[sizes != 0] = 0.8
        else:
            sizes *= 0.8 / np.max(sizes)

        self.elements = QGraphicsItemGroup()
        self.scene.addItem(self.elements)
        if self.attr_color is None:
            self._draw_same_color(sizes)
        elif self.pie_charts:
            self._draw_pie_charts(sizes)
        else:
            self._draw_colored_circles(sizes)

    @property
    def _grid_factors(self):
        return (0.5, sqrt3_2) if self.hexagonal else (0, 1)

    def _draw_same_color(self, sizes):
        fx, fy = self._grid_factors
        color = QColor(64, 64, 64)
        for y in range(self.size_y):
            for x in range(self.size_x - self.hexagonal * (y % 2)):
                r = sizes[x, y]
                n = len(self.get_member_indices(x, y))
                if not r:
                    continue
                ellipse = ColoredCircle(r / 2, color, 0)
                ellipse.setPos(x + (y % 2) * fx, y * fy)
                ellipse.setToolTip(f"{n} instances")
                self.elements.addToGroup(ellipse)

    def _get_color_column(self):
        color_column = \
            self.data.get_column_view(self.attr_color)[0].astype(float,
                                                                 copy=False)
        if self.attr_color.is_discrete:
            with np.errstate(invalid="ignore"):
                int_col = color_column.astype(int)
            int_col[np.isnan(color_column)] = len(self.colors)
        else:
            int_col = np.zeros(len(color_column), dtype=int)
            # The following line is unnecessary because rows with missing
            # numeric data are excluded. Uncomment it if you change SOM to
            # tolerate missing values.
            # int_col[np.isnan(color_column)] = len(self.colors)
            for i, thresh in enumerate(self.thresholds, start=1):
                int_col[color_column >= thresh] = i
        return int_col

    def _tooltip(self, colors, distribution):
        if self.attr_color.is_discrete:
            values = self.attr_color.values
        else:
            values = self._bin_names()
        tot = np.sum(distribution)
        nbhp = "\N{NON-BREAKING HYPHEN}"
        return '<table style="white-space: nowrap">' + "".join(f"""
            <tr>
                <td>
                    <font color={color.name()}>■</font>
                    <b>{escape(val).replace("-", nbhp)}</b>:
                </td>
                <td>
                    {n} ({n / tot * 100:.1f}&nbsp;%)
                </td>
            </tr>
            """ for color, val, n in zip(colors, values, distribution) if n) \
            + "</table>"

    def _draw_pie_charts(self, sizes):
        fx, fy = self._grid_factors
        color_column = self._get_color_column()
        colors = self.colors.qcolors_w_nan
        for y in range(self.size_y):
            for x in range(self.size_x - self.hexagonal * (y % 2)):
                r = sizes[x, y]
                if not r:
                    self.grid_cells[y, x].setToolTip("")
                    continue
                members = self.get_member_indices(x, y)
                color_dist = np.bincount(color_column[members],
                                         minlength=len(colors))
                rel_color_dist = color_dist.astype(float) / len(members)
                pie = PieChart(rel_color_dist, r / 2, colors)
                pie.setToolTip(self._tooltip(colors, color_dist))
                self.elements.addToGroup(pie)
                pie.setPos(x + (y % 2) * fx, y * fy)

    def _draw_colored_circles(self, sizes):
        fx, fy = self._grid_factors
        color_column = self._get_color_column()
        qcolors = self.colors.qcolors_w_nan
        for y in range(self.size_y):
            for x in range(self.size_x - self.hexagonal * (y % 2)):
                r = sizes[x, y]
                if not r:
                    continue
                members = self.get_member_indices(x, y)
                color_dist = color_column[members]
                color_dist = color_dist[color_dist < len(self.colors)]
                if len(color_dist) != len(members):
                    self.Warning.missing_colors(self.attr_color.name)
                bc = np.bincount(color_dist, minlength=len(self.colors))
                color = qcolors[np.argmax(bc)]
                ellipse = ColoredCircle(r / 2, color, np.max(bc) / len(members))
                ellipse.setPos(x + (y % 2) * fx, y * fy)
                ellipse.setToolTip(self._tooltip(qcolors, bc))
                self.elements.addToGroup(ellipse)

    def redraw_grid(self):
        if self.grid is not None:
            self.scene.removeItem(self.grid)
        self.grid = QGraphicsItemGroup()
        self.grid.setZValue(-200)
        self.grid_cells = np.full((self.size_y, self.size_x), None)
        for y in range(self.size_y):
            for x in range(self.size_x - (y % 2) * self.hexagonal):
                if self.hexagonal:
                    cell = QGraphicsPathItem(_hexagon_path)
                    cell.setPos(x + (y % 2) / 2, y * sqrt3_2)
                else:
                    cell = QGraphicsRectItem(x - 0.5, y - 0.5, 1, 1)
                self.grid_cells[y, x] = cell
                cell.setPen(self._grid_pen)
                self.grid.addToGroup(cell)
        self.scene.addItem(self.grid)

    def get_member_indices(self, x, y):
        i, j = self.cells[x, y]
        return self.member_data[i:j]

    def _recompute_som(self):
        if self.cont_x is None:
            return

        som = SOM(
            self.size_x, self.size_y,
            hexagonal=self.hexagonal,
            pca_init=self.initialization == 0,
            random_seed=0 if self.initialization == 2 else None
        )

        class Optimizer(QObject):
            update = Signal(float, np.ndarray, np.ndarray)
            done = Signal(SOM)
            stopped = Signal()
            stop_optimization = False

            def __init__(self, data, som):
                super().__init__()
                self.som = som
                self.data = data

            def callback(self, progress):
                self.update.emit(
                    progress,
                    self.som.weights.copy(), self.som.ssum_weights.copy())
                return not self.stop_optimization

            def run(self):
                try:
                    self.som.fit(self.data, N_ITERATIONS,
                                 callback=self.callback)
                    # Report an exception, but still remove the thread
                finally:
                    self.done.emit(self.som)
                    self.stopped.emit()

        def thread_finished():
            self._optimizer = None
            self._optimizer_thread = None

        self.progressBarInit()

        self._optimizer = Optimizer(self.cont_x, som)
        self._optimizer_thread = QThread()
        self._optimizer_thread.setStackSize(5 * 2 ** 20)
        self._optimizer.update.connect(self.__update)
        self._optimizer.done.connect(self.__done)
        self._optimizer.stopped.connect(self._optimizer_thread.quit)
        self._optimizer.moveToThread(self._optimizer_thread)
        self._optimizer_thread.started.connect(self._optimizer.run)
        self._optimizer_thread.finished.connect(thread_finished)
        self.stop_optimization = False
        self._optimizer_thread.start()

    @Slot(float, object, object)
    def __update(self, _progress, weights, ssum_weights):
        self.progressBarSet(_progress)
        self._assign_instances(weights, ssum_weights)
        self._redraw()

    @Slot(object)
    def __done(self, som):
        self.enable_controls(True)
        self.progressBarFinished()
        self._assign_instances(som.weights, som.ssum_weights)
        self._redraw()
        # This is the first time we know what was selected (assuming that
        # initialization is not set to random)
        if self.__pending_selection is not None:
            self.on_selection_change(self.__pending_selection)
            self.__pending_selection = None
        self.update_output()

    def stop_optimization_and_wait(self):
        if self._optimizer_thread is not None:
            self.stop_optimization = True
            self._optimizer.stop_optimization = True
            self._optimizer_thread.quit()
            self._optimizer_thread.wait()
            self._optimizer_thread = None

    def onDeleteWidget(self):
        self.stop_optimization_and_wait()
        self.clear()
        super().onDeleteWidget()

    def _assign_instances(self, weights, ssum_weights):
        if self.cont_x is None:
            return  # the widget is shutting down while signals still processed
        assignments = SOM.winner_from_weights(
            self.cont_x, weights, ssum_weights, self.hexagonal)
        members = defaultdict(list)
        for i, (x, y) in enumerate(assignments):
            members[(x, y)].append(i)
        members.pop(None, None)
        self.cells = np.empty((self.size_x, self.size_y, 2), dtype=int)
        self.member_data = np.empty(self.cont_x.shape[0], dtype=int)
        index = 0
        for x in range(self.size_x):
            for y in range(self.size_y):
                nmembers = len(members[(x, y)])
                self.member_data[index:index + nmembers] = members[(x, y)]
                self.cells[x, y] = [index, index + nmembers]
                index += nmembers

    def resizeEvent(self, event):
        super().resizeEvent(event)
        self.create_legend()  # re-wrap lines if necessary
        self.rescale()

    def rescale(self):
        if self.legend:
            leg_height = self.legend.boundingRect().height()
            leg_extra = 1.5
        else:
            leg_height = 0
            leg_extra = 1

        vw, vh = self.view.width(), self.view.height() - leg_height
        scale = min(vw / (self.size_x + 1),
                    vh / ((self.size_y + leg_extra) * self._grid_factors[1]))
        self.view.setTransform(QTransform.fromScale(scale, scale))
        if self.hexagonal:
            self.view.setSceneRect(
                0, -1, self.size_x - 1,
                (self.size_y + leg_extra) * sqrt3_2 + leg_height / scale)
        else:
            self.view.setSceneRect(
                -0.25, -0.25, self.size_x - 0.5,
                self.size_y - 0.5 + leg_height / scale)

    def update_output(self):
        if self.data is None:
            self.Outputs.selected_data.send(None)
            self.Outputs.annotated_data.send(None)
            self._set_output_summary(None)
            return

        indices = np.zeros(len(self.data), dtype=int)
        if self.selection is not None and np.any(self.selection):
            for y in range(self.size_y):
                for x in range(self.size_x):
                    rows = self.get_member_indices(x, y)
                    indices[rows] = self.selection[x, y]

        if np.any(indices):
            sel_data = create_groups_table(self.data, indices, False, "Group")
            self.Outputs.selected_data.send(sel_data)
            self._set_output_summary(sel_data)
        else:
            self.Outputs.selected_data.send(None)
            self._set_output_summary(None)

        if np.max(indices) > 1:
            annotated = create_groups_table(self.data, indices)
        else:
            annotated = create_annotated_table(
                self.data, np.flatnonzero(indices))
        self.Outputs.annotated_data.send(annotated)

    def set_color_bins(self):
        if self.attr_color is None:
            self.thresholds = self.bin_labels = self.colors = None
        elif self.attr_color.is_discrete:
            self.thresholds = self.bin_labels = None
            self.colors = self.attr_color.palette
        else:
            col = self.data.get_column_view(self.attr_color)[0].astype(float)
            if self.attr_color.is_time:
                binning = time_binnings(col, min_bins=4)[-1]
            else:
                binning = decimal_binnings(col, min_bins=4)[-1]
            self.thresholds = binning.thresholds[1:-1]
            self.bin_labels = (binning.labels[1:-1], binning.short_labels[1:-1])
            palette = BinnedContinuousPalette.from_palette(
                self.attr_color.palette, binning.thresholds)
            self.colors = palette

    def create_legend(self):
        if self.legend is not None:
            self.scene.removeItem(self.legend)
            self.legend = None
        if self.attr_color is None:
            return

        if self.attr_color.is_discrete:
            names = self.attr_color.values
        else:
            names = self._bin_names()

        items = []
        size = 8
        for name, color in zip(names, self.colors.qcolors):
            item = QGraphicsItemGroup()
            item.addToGroup(
                CanvasRectangle(None, -size / 2, -size / 2, size, size,
                                Qt.gray, color))
            item.addToGroup(CanvasText(None, name, size, 0, Qt.AlignVCenter))
            items.append(item)

        self.legend = wrap_legend_items(
            items, hspacing=20, vspacing=16 + size,
            max_width=self.view.width() - 25)
        self.legend.setFlags(self.legend.ItemIgnoresTransformations)
        self.legend.setTransform(
            QTransform.fromTranslate(-self.legend.boundingRect().width() / 2,
                                     0))
        self.scene.addItem(self.legend)
        self.set_legend_pos()

    def _bin_names(self):
        labels, short_labels = self.bin_labels
        return \
            [f"< {labels[0]}"] \
            + [f"{x} - {y}" for x, y in zip(labels, short_labels[1:])] \
            + [f"≥ {labels[-1]}"]

    def set_legend_pos(self):
        if self.legend is None:
            return
        self.legend.setPos(
            self.size_x / 2,
            (self.size_y + 0.2 + 0.3 * self.hexagonal) * self._grid_factors[1])

    def send_report(self):
        self.report_plot()
        if self.attr_color:
            self.report_caption(
                f"Self-organizing map colored by '{self.attr_color.name}'")


def _draw_hexagon():
    path = QPainterPath()
    s = 0.5 / (np.sqrt(3) / 2)
    path.moveTo(-0.5, -s / 2)
    path.lineTo(-0.5, s / 2)
    path.lineTo(0, s)
    path.lineTo(0.5, s / 2)
    path.lineTo(0.5, -s / 2)
    path.lineTo(0, -s)
    path.lineTo(-0.5, -s / 2)
    return path


_hexagon_path = _draw_hexagon()


if __name__ == "__main__":  # pragma: no cover
    WidgetPreview(OWSOM).run(Table("iris"))
