Orange.widgets.visualize.OWVennDiagram

Complexity

Total Complexity

101

Size/Duplication

Total Lines	533
Duplicated Lines	0 %

29 Methods

Rating	Name	Duplication	Size	Complexity
C	_createDiagram()	0	50	7
A	match()	0	5	2
B	_updateInfo()	0	15	5
F	commit()	0	72	17
A	save_graph()	0	6	1
A	_controlAtIndex()	0	4	1
A	__init__()	0	74	2
B	setData()	0	22	6
A	_invalidate()	0	8	3
A	_on_useidentifiersChanged()	0	8	1
A	_on_selectionChanged()	0	11	4
B	_storeHints()	0	14	5
A	itemsetAttr()	0	9	2
A	items_by_key()	0	7	4
A	_add()	0	14	1
A	items_by_eq()	0	2	1
A	_on_inputAttrActivated()	0	19	4
A	getSettings()	0	3	1
A	_createItemsets()	0	15	4
B	_itemsForInput()	0	20	7
A	_on_itemTextEdited()	0	4	1
A	_setAttributes()	0	12	3
A	invalidateOutput()	0	2	1
B	_remove()	0	24	3
A	_update()	0	13	1
F	handleNewSignals()	0	40	11
B	_restoreHints()	0	19	6
A	_updateItemsets()	0	10	4
A	instance_key()	0	2	1

"""
Venn Diagram Widget
-------------------

"""

import math
import unicodedata

from collections import namedtuple, defaultdict, OrderedDict, Counter
from itertools import count
from functools import reduce
from xml.sax.saxutils import escape

import numpy

The import numpy could not be resolved.

from PyQt4.QtGui import (

The import PyQt4.QtGui could not be resolved.

    QComboBox, QGraphicsScene, QGraphicsView, QGraphicsWidget,
    QGraphicsPathItem, QGraphicsTextItem, QPainterPath, QPainter,
    QTransform, QColor, QBrush, QPen, QStyle, QPalette,
    QApplication
)

from PyQt4.QtCore import Qt, QPointF, QRectF, QLineF

The import PyQt4.QtCore could not be resolved.

from PyQt4.QtCore import pyqtSignal as Signal

The import PyQt4.QtCore could not be resolved.

import Orange.data

from Orange.widgets import widget, gui, settings
from Orange.widgets.utils import itemmodels, colorpalette
from Orange.widgets.io import FileFormats


_InputData = namedtuple("_InputData", ["key", "name", "table"])
_ItemSet = namedtuple("_ItemSet", ["key", "name", "title", "items"])


class OWVennDiagram(widget.OWWidget):
    name = "Venn Diagram"
    description = "A graphical visualization of an overlap of data instances " \
                  "from a collection of input data sets."
    icon = "icons/VennDiagram.svg"

    inputs = [("Data", Orange.data.Table, "setData", widget.Multiple)]
    outputs = [("Selected Data", Orange.data.Table)]

    # Selected disjoint subset indices
    selection = settings.Setting([])
    #: Stored input set hints
    #: {(index, inputname, attributes): (selectedattrname, itemsettitle)}
    #: The 'selectedattrname' can be None
    inputhints = settings.Setting({})
    #: Use identifier columns for instance matching
    useidentifiers = settings.Setting(True)
    autocommit = settings.Setting(True)

    want_graph = True

    def __init__(self, parent=None):
        super().__init__(parent)

        # Diagram update is in progress
        self._updating = False
        # Input update is in progress
        self._inputUpdate = False
        # All input tables have the same domain.
        self.samedomain = True
        # Input datasets in the order they were 'connected'.
        self.data = OrderedDict()
        # Extracted input item sets in the order they were 'connected'
        self.itemsets = OrderedDict()

        # GUI
        box = gui.widgetBox(self.controlArea, "Info")
        self.info = gui.widgetLabel(box, "No data on input\n")

        self.identifiersBox = gui.radioButtonsInBox(
            self.controlArea, self, "useidentifiers", [],
            box="Data Instance Identifiers",
            callback=self._on_useidentifiersChanged
        )
        self.useequalityButton = gui.appendRadioButton(
            self.identifiersBox, "Use instance equality"
        )
        rb = gui.appendRadioButton(
            self.identifiersBox, "Use identifiers"
        )
        self.inputsBox = gui.indentedBox(
            self.identifiersBox, sep=gui.checkButtonOffsetHint(rb)
        )
        self.inputsBox.setEnabled(bool(self.useidentifiers))

        for i in range(5):
            box = gui.widgetBox(self.inputsBox, "Data set #%i" % (i + 1),
                                addSpace=False)
            box.setFlat(True)
            model = itemmodels.VariableListModel(parent=self)
            cb = QComboBox(
                minimumContentsLength=12,
                sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon)
            cb.setModel(model)
            cb.activated[int].connect(self._on_inputAttrActivated)
            box.setEnabled(False)
            # Store the combo in the box for later use.
            box.combo_box = cb
            box.layout().addWidget(cb)

        gui.rubber(self.controlArea)

        gui.auto_commit(self.controlArea, self, "autocommit",
                        "Commit", "Auto commit")

        # Main area view
        self.scene = QGraphicsScene()
        self.view = QGraphicsView(self.scene)
        self.view.setRenderHint(QPainter.Antialiasing)
        self.view.setBackgroundRole(QPalette.Window)
        self.view.setFrameStyle(QGraphicsView.StyledPanel)

        self.mainArea.layout().addWidget(self.view)
        self.vennwidget = VennDiagram()
        self.vennwidget.resize(400, 400)
        self.vennwidget.itemTextEdited.connect(self._on_itemTextEdited)
        self.scene.selectionChanged.connect(self._on_selectionChanged)

        self.scene.addItem(self.vennwidget)

        self.resize(self.controlArea.sizeHint().width() + 550,
                    max(self.controlArea.sizeHint().height(), 550))

        self._queue = []
        self.graphButton.clicked.connect(self.save_graph)

    def setData(self, data, key=None):
        self.error(0)
        if not self._inputUpdate:
            # Store hints only on the first setData call.
            self._storeHints()
            self._inputUpdate = True

        if key in self.data:
            if data is None:
                # Remove the input
                self._remove(key)
            else:
                # Update existing item
                self._update(key, data)
        elif data is not None:
            # TODO: Allow setting more them 5 inputs and let the user

TODO and FIXME comments should generally be avoided.

            # select the 5 to display.
            if len(self.data) == 5:
                self.error(0, "Can only take 5 inputs.")
                return
            # Add a new input
            self._add(key, data)

    def handleNewSignals(self):
        self._inputUpdate = False

        # Check if all inputs are from the same domain.
        domains = [input.table.domain for input in self.data.values()]
        samedomain = all(domain_eq(d1, d2) for d1, d2 in pairwise(domains))

        self.useequalityButton.setEnabled(samedomain)
        self.samedomain = samedomain

        has_identifiers = all(source_attributes(input.table.domain)
                              for input in self.data.values())

        if not samedomain and not self.useidentifiers:
            self.useidentifiers = 1
        elif samedomain and not has_identifiers:
            self.useidentifiers = 0

        incremental = all(inc for _, inc in self._queue)

        if incremental:
            # Only received updated data on existing link.
            self._updateItemsets()
        else:
            # Links were removed and/or added.
            self._createItemsets()
            self._restoreHints()
            self._updateItemsets()

        del self._queue[:]

        self._createDiagram()
        if self.data:
            self.info.setText(
                "{} data sets on input.\n".format(len(self.data)))
        else:
            self.info.setText("No data on input\n")

        self._updateInfo()
        super().handleNewSignals()

    def _invalidate(self, keys=None, incremental=True):
        """
        Invalidate input for a list of input keys.
        """
        if keys is None:
            keys = list(self.data.keys())

        self._queue.extend((key, incremental) for key in keys)

    def itemsetAttr(self, key):
        index = list(self.data.keys()).index(key)
        _, combo = self._controlAtIndex(index)
        model = combo.model()
        attr_index = combo.currentIndex()
        if attr_index >= 0:
            return model[attr_index]
        else:
            return None

    def _controlAtIndex(self, index):
        group_box = self.inputsBox.layout().itemAt(index).widget()
        combo = group_box.combo_box
        return group_box, combo

    def _setAttributes(self, index, attrs):
        box, combo = self._controlAtIndex(index)
        model = combo.model()

        if attrs is None:
            model[:] = []
            box.setEnabled(False)
        else:
            if model[:] != attrs:
                model[:] = attrs

            box.setEnabled(True)

    def _add(self, key, table):
        name = table.name
        index = len(self.data)
        attrs = source_attributes(table.domain)

        self.data[key] = _InputData(key, name, table)

        self._setAttributes(index, attrs)

        self._invalidate([key], incremental=False)

        item = self.inputsBox.layout().itemAt(index)
        box = item.widget()
        box.setTitle("Data set: {}".format(name))

    def _remove(self, key):
        index = list(self.data.keys()).index(key)

        # Clear possible warnings.
        self.warning(index)

        self._setAttributes(index, None)

        del self.data[key]

        layout = self.inputsBox.layout()
        item = layout.takeAt(index)
        layout.addItem(item)
        inputs = list(self.data.values())

        for i in range(5):
            box, _ = self._controlAtIndex(i)
            if i < len(inputs):
                title = "Data set: {}".format(inputs[i].name)
            else:
                title = "Data set #{}".format(i + 1)
            box.setTitle(title)

        self._invalidate([key], incremental=False)

    def _update(self, key, table):
        name = table.name
        index = list(self.data.keys()).index(key)
        attrs = source_attributes(table.domain)

        self.data[key] = self.data[key]._replace(name=name, table=table)

        self._setAttributes(index, attrs)
        self._invalidate([key])

        item = self.inputsBox.layout().itemAt(index)
        box = item.widget()
        box.setTitle("Data set: {}".format(name))

    def _itemsForInput(self, key):
        useidentifiers = self.useidentifiers or not self.samedomain

        def items_by_key(key, input):

This seems to re-define the built-in input.

            attr = self.itemsetAttr(key)
            if attr is not None:
                return [str(inst[attr]) for inst in input.table
                        if not numpy.isnan(inst[attr])]
            else:
                return []

        def items_by_eq(key, input):

This seems to re-define the built-in input.

The argument key seems to be unused.

            return list(map(ComparableInstance, input.table))

        input = self.data[key]

This seems to re-define the built-in input.

        if useidentifiers:
            items = items_by_key(key, input)
        else:
            items = items_by_eq(key, input)
        return items

    def _updateItemsets(self):
        assert list(self.data.keys()) == list(self.itemsets.keys())
        for key, input in list(self.data.items()):

This seems to re-define the built-in input.

            items = self._itemsForInput(key)
            item = self.itemsets[key]
            item = item._replace(items=items)
            name = input.name
            if item.name != name:
                item = item._replace(name=name, title=name)
            self.itemsets[key] = item

    def _createItemsets(self):
        olditemsets = dict(self.itemsets)
        self.itemsets.clear()

        for key, input in self.data.items():

This seems to re-define the built-in input.

            items = self._itemsForInput(key)
            name = input.name
            if key in olditemsets and olditemsets[key].name == name:
                # Reuse the title (which might have been changed by the user)
                title = olditemsets[key].title
            else:
                title = name

            itemset = _ItemSet(key=key, name=name, title=title, items=items)
            self.itemsets[key] = itemset

    def _storeHints(self):
        if self.data:
            self.inputhints.clear()
            for i, (key, input) in enumerate(self.data.items()):

This seems to re-define the built-in input.

                attrs = source_attributes(input.table.domain)
                attrs = tuple(attr.name for attr in attrs)
                selected = self.itemsetAttr(key)
                if selected is not None:
                    attr_name = selected.name
                else:
                    attr_name = None
                itemset = self.itemsets[key]
                self.inputhints[(i, input.name, attrs)] = \
                    (attr_name, itemset.title)

    def _restoreHints(self):
        settings = []

settings is re-defining a name which is already available in the outer-scope (previously defined on line 29).

        for i, (key, input) in enumerate(self.data.items()):

This seems to re-define the built-in input.

            attrs = source_attributes(input.table.domain)
            attrs = tuple(attr.name for attr in attrs)
            hint = self.inputhints.get((i, input.name, attrs), None)
            if hint is not None:
                attr, name = hint
                attr_ind = attrs.index(attr) if attr is not None else -1
                settings.append((attr_ind, name))
            else:
                return

        # all inputs match the stored hints
        for i, key in enumerate(self.itemsets):
            attr, itemtitle = settings[i]
            self.itemsets[key] = self.itemsets[key]._replace(title=itemtitle)
            _, cb = self._controlAtIndex(i)
            cb.setCurrentIndex(attr)

    def _createDiagram(self):
        self._updating = True

        oldselection = list(self.selection)

        self.vennwidget.clear()
        n = len(self.itemsets)
        self.disjoint = disjoint(set(s.items) for s in self.itemsets.values())

The attribute disjoint was defined outside __init__.

        vennitems = []
        colors = colorpalette.ColorPaletteHSV(n)

        for i, (key, item) in enumerate(self.itemsets.items()):

The variable key seems to be unused.

            gr = VennSetItem(text=item.title, count=len(item.items))
            color = colors[i]
            color.setAlpha(100)
            gr.setBrush(QBrush(color))
            gr.setPen(QPen(Qt.NoPen))
            vennitems.append(gr)

        self.vennwidget.setItems(vennitems)

        for i, area in enumerate(self.vennwidget.vennareas()):
            area_items = list(map(str, list(self.disjoint[i])))
            if i:
                area.setText("{0}".format(len(area_items)))

            label = disjoint_set_label(i, n, simplify=False)
            head = "<h4>|{}| = {}</h4>".format(label, len(area_items))
            if len(area_items) > 32:
                items_str = ", ".join(map(escape, area_items[:32]))
                hidden = len(area_items) - 32
                tooltip = ("{}<span>{}, ...</br>({} items not shown)<span>"
                           .format(head, items_str, hidden))
            elif area_items:
                tooltip = "{}<span>{}</span>".format(
                    head,
                    ", ".join(map(escape, area_items))
                )
            else:
                tooltip = head

            area.setToolTip(tooltip)

            area.setPen(QPen(QColor(10, 10, 10, 200), 1.5))
            area.setFlag(QGraphicsPathItem.ItemIsSelectable, True)
            area.setSelected(i in oldselection)

        self._updating = False
        self._on_selectionChanged()

    def _updateInfo(self):
        # Clear all warnings
        self.warning(list(range(5)))

        if not len(self.data):
            self.info.setText("No data on input\n")
        else:
            self.info.setText(
                "{0} data sets on input\n".format(len(self.data)))

        if self.useidentifiers:
            for i, key in enumerate(self.data):
                if not source_attributes(self.data[key].table.domain):
                    self.warning(i, "Data set #{} has no suitable identifiers."
                                 .format(i + 1))

    def _on_selectionChanged(self):
        if self._updating:
            return

        areas = self.vennwidget.vennareas()
        indices = [i for i, area in enumerate(areas)
                   if area.isSelected()]

        self.selection = indices

        self.invalidateOutput()

    def _on_useidentifiersChanged(self):
        self.inputsBox.setEnabled(self.useidentifiers == 1)
        # Invalidate all itemsets
        self._invalidate()
        self._updateItemsets()
        self._createDiagram()

        self._updateInfo()

    def _on_inputAttrActivated(self, attr_index):

The argument attr_index seems to be unused.

        combo = self.sender()
        # Find the input index to which the combo box belongs
        # (they are reordered when removing inputs).
        index = None
        inputs = list(self.data.items())
        for i in range(len(inputs)):
            _, c = self._controlAtIndex(i)
            if c is combo:
                index = i
                break

        assert (index is not None)

There is an unnecessary parenthesis after assert.

        key, _ = inputs[index]

        self._invalidate([key])
        self._updateItemsets()
        self._createDiagram()

    def _on_itemTextEdited(self, index, text):
        text = str(text)
        key = list(self.itemsets.keys())[index]
        self.itemsets[key] = self.itemsets[key]._replace(title=text)

    def invalidateOutput(self):
        self.commit()

    def commit(self):
        selected_subsets = []

        selected_items = reduce(
            set.union, [self.disjoint[index] for index in self.selection],
            set()
        )
        def match(val):
            if numpy.isnan(val):
                return False
            else:
                return str(val) in selected_items

        source_var = Orange.data.StringVariable("source")
        item_id_var = Orange.data.StringVariable("item_id")

        names = [itemset.title.strip() for itemset in self.itemsets.values()]
        names = uniquify(names)

        for i, (key, input) in enumerate(self.data.items()):

This seems to re-define the built-in input.

            if self.useidentifiers:
                attr = self.itemsetAttr(key)
                if attr is not None:
                    mask = list(map(match, (inst[attr] for inst in input.table)))
                else:
                    mask = [False] * len(input.table)

                def instance_key(inst):
                    return str(inst[attr])
            else:
                mask = [ComparableInstance(inst) in selected_items
                        for inst in input.table]
                _map = {item: str(i) for i, item in enumerate(selected_items)}

                def instance_key(inst):
                    return _map[ComparableInstance(inst)]

            mask = numpy.array(mask, dtype=bool)
            subset = Orange.data.Table(input.table.domain,
                                       input.table[mask])
            subset.ids = input.table.ids[mask]
            if len(subset) == 0:
                continue

            # add columns with source table id and set id

            id_column = numpy.array([[instance_key(inst)] for inst in subset],
                                    dtype=object)
            source_names = numpy.array([[names[i]]] * len(subset),
                                       dtype=object)

            subset = append_column(subset, "M", source_var, source_names)
            subset = append_column(subset, "M", item_id_var, id_column)

            selected_subsets.append(subset)

        if selected_subsets:
            data = table_concat(selected_subsets)
            # Get all variables which are not constant between the same
            # item set
            varying = varying_between(data, [item_id_var])

            if source_var in varying:
                varying.remove(source_var)

            data = reshape_wide(data, varying, [item_id_var], [source_var])
            # remove the temporary item set id column
            data = drop_columns(data, [item_id_var])
        else:
            data = None

        self.send("Selected Data", data)

    def getSettings(self, *args, **kwargs):
        self._storeHints()
        return super().getSettings(self, *args, **kwargs)

    def save_graph(self):
        from Orange.widgets.data.owsave import OWSave

        save_img = OWSave(parent=self, data=self.scene,
                          file_formats=FileFormats.img_writers)
        save_img.exec_()


def pairwise(iterable):
    """
    Return an iterator over consecutive pairs in `iterable`.

    >>> list(pairwise([1, 2, 3, 4])
    [(1, 2), (2, 3), (3, 4)]

    """
    it = iter(iterable)
    first = next(it)
    for second in it:
        yield first, second
        first = second


# Custom domain comparison (domains do not seem to compare equal
# even if they have exactly the same variables).
# TODO: What about metas.

TODO and FIXME comments should generally be avoided.

def domain_eq(d1, d2):
    return tuple(d1) == tuple(d2)


# Comparing/hashing Orange.data.Instance across domains ignoring metas.
class ComparableInstance:
    __slots__ = ["inst", "domain"]

    def __init__(self, inst):
        self.inst = inst
        self.domain = inst.domain

    def __hash__(self):
        return hash(self.inst.x.data.tobytes())

    def __eq__(self, other):
        # XXX: comparing NaN with different payload

TODO and FIXME comments should generally be avoided.

        return (domain_eq(self.domain, other.domain)
                and self.inst.x.data.tobytes() == other.inst.x.data.tobytes())

    def __iter__(self):
        return iter(self.inst)

    def __repr__(self):
        return repr(self.inst)

    def __str__(self):
        return str(self.inst)


def table_concat(tables):
    """
    Concatenate a list of tables.

    The resulting table will have a union of all attributes of `tables`.

    """
    attributes = []
    class_vars = []
    metas = []
    variables_seen = set()

    for table in tables:
        attributes.extend(v for v in table.domain.attributes
                          if v not in variables_seen)
        variables_seen.update(table.domain.attributes)

        class_vars.extend(v for v in table.domain.class_vars
                          if v not in variables_seen)
        variables_seen.update(table.domain.class_vars)

        metas.extend(v for v in table.domain.metas
                     if v not in variables_seen)

        variables_seen.update(table.domain.metas)

    domain = Orange.data.Domain(attributes, class_vars, metas)
    new_table = Orange.data.Table(domain)

    for table in tables:
        new_table.extend(Orange.data.Table.from_table(domain, table))

    return new_table


def copy_descriptor(descriptor, newname=None):
    """
    Create a copy of the descriptor.

    If newname is not None the new descriptor will have the same
    name as the input.

    """
    if newname is None:
        newname = descriptor.name

    if descriptor.is_discrete:
        newf = Orange.data.DiscreteVariable(
            newname,
            values=descriptor.values,
            base_value=descriptor.base_value,
            ordered=descriptor.ordered,
        )
        newf.attributes = dict(descriptor.attributes)

    elif descriptor.is_continuous:
        newf = Orange.data.ContinuousVariable(newname)
        newf.number_of_decimals = descriptor.number_of_decimals
        newf.attributes = dict(descriptor.attributes)

    else:
        newf = type(descriptor)(newname)
        newf.attributes = dict(descriptor.attributes)

    return newf


def reshape_wide(table, varlist, idvarlist, groupvarlist):
    """
    Reshape a data table into a wide format.

    :param Orange.data.Table table:
        Source data table in long format.
    :param varlist:
        A list of variables to reshape.
    :param list idvarlist:
        A list of variables in `table` uniquely identifying multiple
        records in `table` (i.e. subject id).
    :param groupvarlist:
        A list of variables differentiating multiple records
        (i.e. conditions).

    """
    def inst_key(inst, vars):

This seems to re-define the built-in vars.

        return tuple(str(inst[var]) for var in vars)

    instance_groups = [inst_key(inst, groupvarlist) for inst in table]
    # A list of groups (for each element in a group the varying variable
    # will be duplicated)
    groups = list(unique(instance_groups))
    group_names = [", ".join(group) for group in groups]

    # A list of instance ids (subject ids)
    # Each instance in the output will correspond to one of these ids)
    instance_ids = [inst_key(inst, idvarlist) for inst in table]
    ids = list(unique(instance_ids))

    # an mapping from ids to an list of input instance indices
    # each instance in this list belongs to one group (but not all
    # groups need to be present).
    inst_by_id = defaultdict(list)

    for i in range(len(table)):
        inst_id = instance_ids[i]
        inst_by_id[inst_id].append(i)

    newfeatures = []
    newclass_vars = []
    newmetas = []
    expanded_features = {}

    def expanded(feat):
        return [copy_descriptor(feat, newname="%s (%s)" %
                                (feat.name, group_name))
                for group_name in group_names]

    for feat in table.domain.attributes:
        if feat in varlist:
            features = expanded(feat)
            newfeatures.extend(features)
            expanded_features[feat] = dict(zip(groups, features))
        elif feat not in groupvarlist:
            newfeatures.append(feat)

    for feat in table.domain.class_vars:
        if feat in varlist:
            features = expanded(feat)
            newclass_vars.extend(features)
            expanded_features[feat] = dict(zip(groups, features))
        elif feat not in groupvarlist:
            newclass_vars.append(feat)

    for meta in table.domain.metas:
        if meta in varlist:
            metas = expanded(meta)
            newmetas.extend(metas)
            expanded_features[meta] = dict(zip(groups, metas))
        elif meta not in groupvarlist:
            newmetas.append(meta)

    domain = Orange.data.Domain(newfeatures, newclass_vars, newmetas)
    prototype_indices = [inst_by_id[inst_id][0] for inst_id in ids]
    newtable = Orange.data.Table.from_table(domain, table)[prototype_indices]
    in_expanded = set(f for efd in expanded_features.values() for f in efd.values())

    for i, inst_id in enumerate(ids):
        indices = inst_by_id[inst_id]
        instance = newtable[i]

        for var in domain.variables + domain.metas:
            if var in idvarlist or var in in_expanded:
                continue
            if numpy.isnan(instance[var]):
                for ind in indices:
                    if not numpy.isnan(table[ind, var]):
                        newtable[i, var] = table[ind, var]

        for index in indices:
            source_inst = table[index]
            group = instance_groups[index]
            for source_var in varlist:
                newf = expanded_features[source_var][group]
                instance[newf] = source_inst[source_var]

    return newtable


def unique(seq):
    """
    Return an iterator over unique items of `seq`.

    .. note:: Items must be hashable.

    """
    seen = set()
    for item in seq:
        if item not in seen:
            yield item
            seen.add(item)

from Orange.widgets.data.owmergedata import group_table_indices


def unique_non_nan(ar):
    # metas have sometimes object dtype, but values are numpy floats
    ar = ar.astype('float64')
    uniq = numpy.unique(ar)
    return uniq[~numpy.isnan(uniq)]


def varying_between(table, idvarlist):
    """
    Return a list of all variables with non constant values between
    groups defined by `idvarlist`.

    """
    def inst_key(inst, vars):

This seems to re-define the built-in vars.

The variable inst_key seems to be unused.

        return tuple(str(inst[var]) for var in vars)

    excluded = set(idvarlist)
    all_possible = [var for var in table.domain.variables + table.domain.metas
                    if var not in excluded]
    candidate_set = set(all_possible)

    idmap = group_table_indices(table, idvarlist)
    values = {}
    varying = set()
    for indices in idmap.values():
        subset = table[indices]
        for var in list(candidate_set):
            values = subset[:, var]
            values, _ = subset.get_column_view(var)

            if var.is_string:
                uniq = set(values)
            else:
                uniq = unique_non_nan(values)

            if len(uniq) > 1:
                varying.add(var)
                candidate_set.remove(var)

    return sorted(varying, key=all_possible.index)


def uniquify(strings):
    """
    Return a list of unique strings.

    The string at i'th position will have the same prefix as strings[i]
    with an appended suffix to make the item unique (if necessary).

    >>> uniquify(["cat", "dog", "cat"])
    ["cat 1", "dog", "cat 2"]

    """
    counter = Counter(strings)
    counts = defaultdict(count)
    newstrings = []
    for string in strings:
        if counter[string] > 1:
            newstrings.append(string + (" %i" % (next(counts[string]) + 1)))
        else:
            newstrings.append(string)

    return newstrings


def string_attributes(domain):
    """
    Return all string attributes from the domain.
    """
    return [attr for attr in domain.variables + domain.metas
            if attr.is_string]


def discrete_attributes(domain):
    """
    Return all discrete attributes from the domain.
    """
    return [attr for attr in domain.variables + domain.metas
                 if attr.is_discrete]


def source_attributes(domain):
    """
    Return all suitable attributes for the venn diagram.
    """
    return string_attributes(domain)  # + discrete_attributes(domain)


def disjoint(sets):
    """
    Return all disjoint subsets.
    """
    sets = list(sets)
    n = len(sets)
    disjoint_sets = [None] * (2 ** n)
    for i in range(2 ** n):
        key = setkey(i, n)
        included = [s for s, inc in zip(sets, key) if inc]
        excluded = [s for s, inc in zip(sets, key) if not inc]
        if any(included):
            s = reduce(set.intersection, included)
        else:
            s = set()

        s = reduce(set.difference, excluded, s)

        disjoint_sets[i] = s

    return disjoint_sets


def disjoint_set_label(i, n, simplify=False):

The argument i seems to be unused.

    """
    Return a html formated label for a disjoint set indexed by `i`.
    """
    intersection = unicodedata.lookup("INTERSECTION")
    # comp = unicodedata.lookup("COMPLEMENT")  #
    # This depends on the font but the unicode complement in
    # general does not look nice in a super script so we use
    # plain c instead.
    comp = "c"

    def label_for_index(i):
        return chr(ord("A") + i)

    if simplify:
        return "".join(label_for_index(i) for i, b in enumerate(setkey(i, n))
                       if b)
    else:
        return intersection.join(label_for_index(i) +
                                 ("" if b else "<sup>" + comp + "</sup>")
                                 for i, b in enumerate(setkey(i, n)))


class VennSetItem(QGraphicsPathItem):
    def __init__(self, parent=None, text=None, count=None):

count is re-defining a name which is already available in the outer-scope (previously defined on line 11).

        super(VennSetItem, self).__init__(parent)
        self.text = text
        self.count = count


# TODO: Use palette's selected/highligted text / background colors to

TODO and FIXME comments should generally be avoided.

# indicate selection

class VennIntersectionArea(QGraphicsPathItem):
    def __init__(self, parent=None, text=""):

The argument text seems to be unused.

        super(QGraphicsPathItem, self).__init__(parent)

The first argument passed to super() should be the super-class name, but QGraphicsPathItem was given.

        self.setAcceptHoverEvents(True)
        self.setPen(QPen(Qt.NoPen))

        self.text = QGraphicsTextItem(self)
        layout = self.text.document().documentLayout()
        layout.documentSizeChanged.connect(self._onLayoutChanged)

        self._text = ""
        self._anchor = QPointF()

    def setText(self, text):
        if self._text != text:
            self._text = text
            self.text.setPlainText(text)

    def text(self):

This method seems to be hidden by an attribute defined in Orange.widgets.visualize.owvenndiagram on line 954.

        return self._text

    def setTextAnchor(self, pos):
        if self._anchor != pos:
            self._anchor = pos
            self._updateTextAnchor()

    def hoverEnterEvent(self, event):
        self.setZValue(self.zValue() + 1)
        return QGraphicsPathItem.hoverEnterEvent(self, event)

    def hoverLeaveEvent(self, event):
        self.setZValue(self.zValue() - 1)
        return QGraphicsPathItem.hoverLeaveEvent(self, event)

    def mousePressEvent(self, event):
        if event.button() == Qt.LeftButton:
            if event.modifiers() & Qt.AltModifier:
                self.setSelected(False)
            elif event.modifiers() & Qt.ControlModifier:
                self.setSelected(not self.isSelected())
            elif event.modifiers() & Qt.ShiftModifier:
                self.setSelected(True)
            else:
                for area in self.parentWidget().vennareas():
                    area.setSelected(False)
                self.setSelected(True)

    def mouseReleaseEvent(self, event):
        pass

    def paint(self, painter, option, widget=None):

widget is re-defining a name which is already available in the outer-scope (previously defined on line 29).

The argument widget seems to be unused.

        painter.save()
        path = self.path()
        brush = QBrush(self.brush())
        pen = QPen(self.pen())

        if option.state & QStyle.State_Selected:
            pen.setColor(Qt.red)
            brush.setStyle(Qt.DiagCrossPattern)
            brush.setColor(QColor(40, 40, 40, 100))

        elif option.state & QStyle.State_MouseOver:
            pen.setColor(Qt.blue)

        if option.state & QStyle.State_MouseOver:
            brush.setColor(QColor(100, 100, 100, 100))
            if brush.style() == Qt.NoBrush:
                # Make sure the highlight is actually visible.
                brush.setStyle(Qt.SolidPattern)

        painter.setPen(pen)
        painter.setBrush(brush)
        painter.drawPath(path)
        painter.restore()

    def itemChange(self, change, value):
        if change == QGraphicsPathItem.ItemSelectedHasChanged:
            self.setZValue(self.zValue() + (1 if value else -1))
        return QGraphicsPathItem.itemChange(self, change, value)

    def _updateTextAnchor(self):
        rect = self.text.boundingRect()
        pos = anchor_rect(rect, self._anchor)
        self.text.setPos(pos)

    def _onLayoutChanged(self):
        self._updateTextAnchor()


class GraphicsTextEdit(QGraphicsTextItem):
    #: Edit triggers
    NoEditTriggers, DoubleClicked = 0, 1

    editingFinished = Signal()
    editingStarted = Signal()

    documentSizeChanged = Signal()

    def __init__(self, *args, **kwargs):
        super(GraphicsTextEdit, self).__init__(*args, **kwargs)
        self.setTabChangesFocus(True)
        self._edittrigger = GraphicsTextEdit.DoubleClicked
        self._editing = False
        self.document().documentLayout().documentSizeChanged.connect(
            self.documentSizeChanged
        )

    def mouseDoubleClickEvent(self, event):
        super(GraphicsTextEdit, self).mouseDoubleClickEvent(event)
        if self._edittrigger == GraphicsTextEdit.DoubleClicked:
            self._start()

    def focusOutEvent(self, event):
        super(GraphicsTextEdit, self).focusOutEvent(event)

        if self._editing:
            self._end()

    def _start(self):
        self._editing = True
        self.setTextInteractionFlags(Qt.TextEditorInteraction)
        self.setFocus(Qt.MouseFocusReason)
        self.editingStarted.emit()

    def _end(self):
        self._editing = False
        self.setTextInteractionFlags(Qt.NoTextInteraction)
        self.editingFinished.emit()


class VennDiagram(QGraphicsWidget):
    # rect and petal are for future work
    Circle, Ellipse, Rect, Petal = 1, 2, 3, 4

    TitleFormat = "<center><h4>{0}</h4>{1}</center>"

    selectionChanged = Signal()
    itemTextEdited = Signal(int, str)

    def __init__(self, parent=None):
        super(VennDiagram, self).__init__(parent)
        self.shapeType = VennDiagram.Circle

        self._setup()

    def _setup(self):
        self._items = []
        self._vennareas = []
        self._textitems = []

    def item(self, index):
        return self._items[index]

    def items(self):
        return list(self._items)

    def count(self):
        return len(self._items)

    def setItems(self, items):
        if self._items:
            self.clear()

        self._items = list(items)

The attribute _items was defined outside __init__.

        for item in self._items:
            item.setParentItem(self)
            item.setVisible(True)

        fmt = self.TitleFormat.format

        font = self.font()
        font.setPixelSize(14)

        for item in items:
            text = GraphicsTextEdit(self)
            text.setFont(font)
            text.setDefaultTextColor(QColor("#333"))
            text.setHtml(fmt(escape(item.text), item.count))
            text.adjustSize()
            text.editingStarted.connect(self._on_editingStarted)
            text.editingFinished.connect(self._on_editingFinished)
            text.documentSizeChanged.connect(
                self._on_itemTextSizeChanged
            )

            self._textitems.append(text)

        self._vennareas = [

The attribute _vennareas was defined outside __init__.

            VennIntersectionArea(parent=self)
            for i in range(2 ** len(items))
        ]
        self._subsettextitems = [

The attribute _subsettextitems was defined outside __init__.

            QGraphicsTextItem(parent=self)
            for i in range(2 ** len(items))
        ]

        self._updateLayout()

    def clear(self):
        scene = self.scene()
        items = self.vennareas() + list(self.items()) + self._textitems

        for item in self._textitems:
            item.editingStarted.disconnect(self._on_editingStarted)
            item.editingFinished.disconnect(self._on_editingFinished)
            item.documentSizeChanged.disconnect(
                self._on_itemTextSizeChanged
            )

        self._items = []

The attribute _items was defined outside __init__.

        self._vennareas = []

The attribute _vennareas was defined outside __init__.

        self._textitems = []

The attribute _textitems was defined outside __init__.

        for item in items:
            item.setVisible(False)
            item.setParentItem(None)
            if scene is not None:
                scene.removeItem(item)

    def vennareas(self):
        return list(self._vennareas)

    def setFont(self, font):
        if self._font != font:
            self.prepareGeometryChange()
            self._font = font

The attribute _font was defined outside __init__.

            for item in self.items():
                item.setFont(font)

    def _updateLayout(self):
        rect = self.geometry()
        n = len(self._items)
        if not n:
            return

        regions = venn_diagram(n, shape=self.shapeType)

        # The y axis in Qt points downward
        transform = QTransform().scale(1, -1)
        regions = list(map(transform.map, regions))

        union_brect = reduce(QRectF.united,
                             (path.boundingRect() for path in regions))

        scalex = rect.width() / union_brect.width()
        scaley = rect.height() / union_brect.height()
        scale = min(scalex, scaley)

        transform = QTransform().scale(scale, scale)

        regions = [transform.map(path) for path in regions]

        center = rect.width() / 2, rect.height() / 2
        for item, path in zip(self.items(), regions):
            item.setPath(path)
            item.setPos(*center)

        intersections = venn_intersections(regions)
        assert len(intersections) == 2 ** n
        assert len(self.vennareas()) == 2 ** n

        anchors = [(0, 0)] + subset_anchors(self._items)

        anchor_transform = QTransform().scale(rect.width(), -rect.height())
        for i, area in enumerate(self.vennareas()):
            area.setPath(intersections[setkey(i, n)])
            area.setPos(*center)
            x, y = anchors[i]
            anchor = anchor_transform.map(QPointF(x, y))
            area.setTextAnchor(anchor)
            area.setZValue(30)

        self._updateTextAnchors()

    def _updateTextAnchors(self):
        n = len(self._items)

        items = self._items
        dist = 15

        shape = reduce(QPainterPath.united, [item.path() for item in items])
        brect = shape.boundingRect()
        bradius = max(brect.width() / 2, brect.height() / 2)

        center = self.boundingRect().center()

        anchors = _category_anchors(items)
        self._textanchors = []

The attribute _textanchors was defined outside __init__.

        for angle, anchor_h, anchor_v in anchors:
            line = QLineF.fromPolar(bradius, angle)
            ext = QLineF.fromPolar(dist, angle)
            line = QLineF(line.p1(), line.p2() + ext.p2())
            line = line.translated(center)

            anchor_pos = line.p2()
            self._textanchors.append((anchor_pos, anchor_h, anchor_v))

        for i in range(n):
            self._updateTextItemPos(i)

    def _updateTextItemPos(self, i):
        item = self._textitems[i]
        anchor_pos, anchor_h, anchor_v = self._textanchors[i]
        rect = item.boundingRect()
        pos = anchor_rect(rect, anchor_pos, anchor_h, anchor_v)
        item.setPos(pos)

    def setGeometry(self, geometry):
        super(VennDiagram, self).setGeometry(geometry)
        self._updateLayout()

    def paint(self, painter, option, w):
        super(VennDiagram, self).paint(painter, option, w)
#         painter.drawRect(self.boundingRect())

    def _on_editingStarted(self):
        item = self.sender()
        index = self._textitems.index(item)
        text = self._items[index].text
        item.setTextWidth(-1)
        item.setHtml(self.TitleFormat.format(escape(text), "<br/>"))

    def _on_editingFinished(self):
        item = self.sender()
        index = self._textitems.index(item)
        text = item.toPlainText()
        if text != self._items[index].text:
            self._items[index].text = text

            self.itemTextEdited.emit(index, text)

        item.setHtml(
            self.TitleFormat.format(escape(text), self._items[index].count))
        item.adjustSize()

    def _on_itemTextSizeChanged(self):
        item = self.sender()
        index = self._textitems.index(item)
        self._updateTextItemPos(index)


def anchor_rect(rect, anchor_pos,
                anchor_h=Qt.AnchorHorizontalCenter,
                anchor_v=Qt.AnchorVerticalCenter):

    if anchor_h == Qt.AnchorLeft:
        x = anchor_pos.x()
    elif anchor_h == Qt.AnchorHorizontalCenter:
        x = anchor_pos.x() - rect.width() / 2
    elif anchor_h == Qt.AnchorRight:
        x = anchor_pos.x() - rect.width()
    else:
        raise ValueError(anchor_h)

    if anchor_v == Qt.AnchorTop:
        y = anchor_pos.y()
    elif anchor_v == Qt.AnchorVerticalCenter:
        y = anchor_pos.y() - rect.height() / 2
    elif anchor_v == Qt.AnchorBottom:
        y = anchor_pos.y() - rect.height()
    else:
        raise ValueError(anchor_v)

    return QPointF(x, y)


def radians(angle):
    return 2 * math.pi * angle / 360


def unit_point(x, r=1.0):
    x = radians(x)
    return (r * math.cos(x), r * math.sin(x))


def _category_anchors(shapes):
    n = len(shapes)
    return _CATEGORY_ANCHORS[n - 1]


# (angle, horizontal anchor, vertical anchor)
_CATEGORY_ANCHORS = (
    # n == 1
    ((90, Qt.AnchorHorizontalCenter, Qt.AnchorBottom),),
    # n == 2
    ((180, Qt.AnchorRight, Qt.AnchorVerticalCenter),
     (0, Qt.AnchorLeft, Qt.AnchorVerticalCenter)),
    # n == 3
    ((150, Qt.AnchorRight, Qt.AnchorBottom),
     (30, Qt.AnchorLeft, Qt.AnchorBottom),
     (270, Qt.AnchorHorizontalCenter, Qt.AnchorTop)),
    # n == 4
    ((270 + 45, Qt.AnchorLeft, Qt.AnchorTop),
     (270 - 45, Qt.AnchorRight, Qt.AnchorTop),
     (90 - 15, Qt.AnchorLeft, Qt.AnchorBottom),
     (90 + 15, Qt.AnchorRight, Qt.AnchorBottom)),
    # n == 5
    ((90 - 5, Qt.AnchorHorizontalCenter, Qt.AnchorBottom),
     (18 - 5, Qt.AnchorLeft, Qt.AnchorVerticalCenter),
     (306 - 5, Qt.AnchorLeft, Qt.AnchorTop),
     (234 - 5, Qt.AnchorRight, Qt.AnchorTop),
     (162 - 5, Qt.AnchorRight, Qt.AnchorVerticalCenter),)
)


def subset_anchors(shapes):
    n = len(shapes)
    if n == 1:
        return [(0, 0)]
    elif n == 2:
        return [unit_point(180, r=1/3),
                unit_point(0, r=1/3),
                (0, 0)]
    elif n == 3:
        return [unit_point(150, r=0.35),  # A
                unit_point(30, r=0.35),   # B
                unit_point(90, r=0.27),   # AB
                unit_point(270, r=0.35),  # C
                unit_point(210, r=0.27),  # AC
                unit_point(330, r=0.27),  # BC
                unit_point(0, r=0),       # ABC
                ]
    elif n == 4:
        anchors = [
            (0.400, 0.110),    # A
            (-0.400, 0.110),   # B
            (0.000, -0.285),   # AB
            (0.180, 0.330),    # C
            (0.265, 0.205),    # AC
            (-0.240, -0.110),  # BC
            (-0.100, -0.190),  # ABC
            (-0.180, 0.330),   # D
            (0.240, -0.110),   # AD
            (-0.265, 0.205),   # BD
            (0.100, -0.190),   # ABD
            (0.000, 0.250),    # CD
            (0.153, 0.090),    # ACD
            (-0.153, 0.090),   # BCD
            (0.000, -0.060),   # ABCD
        ]
        return anchors

    elif n == 5:
        anchors = [None] * 32
        # Base anchors
        A = (0.033, 0.385)
        AD = (0.095, 0.250)
        AE = (-0.100, 0.265)
        ACE = (-0.130, 0.220)
        ADE = (0.010, 0.225)
        ACDE = (-0.095, 0.175)
        ABCDE = (0.0, 0.0)

        anchors[-1] = ABCDE

        bases = [(0b00001, A),
                 (0b01001, AD),
                 (0b10001, AE),
                 (0b10101, ACE),
                 (0b11001, ADE),
                 (0b11101, ACDE)]

        for i in range(5):
            for index, anchor in bases:
                index = bit_rot_left(index, i, bits=5)
                assert anchors[index] is None
                anchors[index] = rotate_point(anchor, - 72 * i)

        assert all(anchors[1:])
        return anchors[1:]


def bit_rot_left(x, y, bits=32):
    mask = 2 ** bits - 1
    x_masked = x & mask
    return (x << y) & mask | (x_masked >> bits - y)


def rotate_point(p, angle):
    r = radians(angle)
    R = numpy.array([[math.cos(r), -math.sin(r)],
                     [math.sin(r), math.cos(r)]])
    x, y = numpy.dot(R, p)
    return (float(x), float(y))


def line_extended(line, distance):
    """
    Return an QLineF extended by `distance` units in the positive direction.
    """
    angle = line.angle() / 360 * 2 * math.pi
    dx, dy = unit_point(angle, r=distance)
    return QLineF(line.p1(), line.p2() + QPointF(dx, dy))


def circle_path(center, r=1.0):
    return ellipse_path(center, r, r, rotation=0)


def ellipse_path(center, a, b, rotation=0):
    if not isinstance(center, QPointF):
        center = QPointF(*center)

    brect = QRectF(-a, -b, 2 * a, 2 * b)

    path = QPainterPath()
    path.addEllipse(brect)

    if rotation != 0:
        transform = QTransform().rotate(rotation)
        path = transform.map(path)

    path.translate(center)
    return path


# TODO: Should include anchors for text layout (both inside and outside).

TODO and FIXME comments should generally be avoided.

# for each item {path: QPainterPath,
#                text_anchors: [{center}] * (2 ** n)
#                mayor_axis: QLineF,
#                boundingRect QPolygonF (with 4 vertices)}
#
# Should be a new class with overloads for ellipse/circle, rect, and petal
# shapes, should store all constructor parameters, rotation, center,
# mayor/minor axis.


def venn_diagram(n, shape=VennDiagram.Circle):

The argument shape seems to be unused.

    if n < 1 or n > 5:
        raise ValueError()

    paths = []

    if n == 1:
        paths = [circle_path(center=(0, 0), r=0.5)]
    elif n == 2:
        angles = [180, 0]
        paths = [circle_path(center=unit_point(x, r=1/6), r=1/3)
                 for x in angles]
    elif n == 3:
        angles = [150 - 120 * i for i in range(3)]
        paths = [circle_path(center=unit_point(x, r=1/6), r=1/3)
                 for x in angles]
    elif n == 4:
        # Constants shamelessly stolen from VennDiagram R package
        paths = [
            ellipse_path((0.65 - 0.5, 0.47 - 0.5), 0.35, 0.20, 45),
            ellipse_path((0.35 - 0.5, 0.47 - 0.5), 0.35, 0.20, 135),
            ellipse_path((0.5 - 0.5, 0.57 - 0.5), 0.35, 0.20, 45),
            ellipse_path((0.5 - 0.5, 0.57 - 0.5), 0.35, 0.20, 134),
        ]
    elif n == 5:
        # Constants shamelessly stolen from VennDiagram R package
        d = 0.13
        a, b = 0.24, 0.48
        a, b = b, a
        a, b = 0.48, 0.24
        paths = [ellipse_path(unit_point((1 - i) * 72, r=d),
                              a, b, rotation=90 - (i * 72))
                 for i in range(5)]

    return paths


def setkey(intval, n):
    return tuple(bool(intval & (2 ** i)) for i in range(n))


def keyrange(n):
    if n < 0:
        raise ValueError()

    for i in range(2 ** n):
        yield setkey(i, n)


def venn_intersections(paths):
    n = len(paths)
    return {key: venn_intersection(paths, key) for key in keyrange(n)}


def venn_intersection(paths, key):
    if not any(key):
        return QPainterPath()

    # first take the intersection of all included paths
    path = reduce(QPainterPath.intersected,
                  (path for path, included in zip(paths, key) if included))

    # subtract all the excluded sets (i.e. take the intersection
    # with the excluded set complements)
    path = reduce(QPainterPath.subtracted,
                  (path for path, included in zip(paths, key) if not included),
                  path)

    return path


def append_column(data, where, variable, column):
    X, Y, M, W = data.X, data.Y, data.metas, data.W
    domain = data.domain
    attr = domain.attributes
    class_vars = domain.class_vars
    metas = domain.metas

    if where == "X":
        attr = attr + (variable,)
        X = numpy.hstack((X, column))
    elif where == "Y":
        class_vars = class_vars + (variable,)
        Y = numpy.hstack((Y, column))
    elif where == "M":
        metas = metas + (variable,)
        M = numpy.hstack((M, column))
    else:
        raise ValueError
    domain = Orange.data.Domain(attr, class_vars, metas)
    table = Orange.data.Table.from_numpy(domain, X, Y, M, W if W.size else None)
    table.ids = data.ids
    return table


def drop_columns(data, columns):
    columns = set(data.domain[col] for col in columns)

    def filter_vars(vars):

This seems to re-define the built-in vars.

        return tuple(var for var in vars if var not in columns)

    domain = Orange.data.Domain(
        filter_vars(data.domain.attributes),
        filter_vars(data.domain.class_vars),
        filter_vars(data.domain.metas)
    )
    return Orange.data.Table.from_table(domain, data)


def test():
    import sklearn.cross_validation as skl_cross_validation

The import sklearn.cross_validation could not be resolved.

    app = QApplication([])
    w = OWVennDiagram()
    data = Orange.data.Table("brown-selected")
    data = append_column(data, "M", Orange.data.StringVariable("Test"),
                         numpy.arange(len(data)).reshape(-1, 1) % 30)

    indices = skl_cross_validation.ShuffleSplit(
        len(data), n_iter=5, test_size=0.7
    )

    indices = iter(indices)

    def select(data):
        sample, _ = next(indices)
        return data[sample]

    d1 = select(data)
    d2 = select(data)
    d3 = select(data)
    d4 = select(data)
    d5 = select(data)

    for i, data in enumerate([d1, d2, d3, d4, d5]):
        data.name = chr(ord("A") + i)
        w.setData(data, key=i)

    w.handleNewSignals()
    w.show()
    app.exec_()

    del w
    app.processEvents()
    return app


def test1():
    app = QApplication([])
    w = OWVennDiagram()
    data1 = Orange.data.Table("brown-selected")
    data2 = Orange.data.Table("brown-selected")
    w.setData(data1, 1)
    w.setData(data2, 2)
    w.handleNewSignals()

    w.show()
    w.raise_()
    app.exec_()

    del w
    return app

if __name__ == "__main__":
    test()