class OWMDS(widget.OWWidget):
name = "MDS"
description = "Two-dimensional data projection by multidimensional " \
"scaling constructed from a distance matrix."
icon = "icons/MDS.svg"
inputs = [("Data", Orange.data.Table, "set_data", widget.Default),
("Distances", Orange.misc.DistMatrix, "set_disimilarity"),
("Data Subset", Orange.data.Table, "set_subset_data")]
outputs = [("Selected Data", Orange.data.Table, widget.Default),
("Data", Orange.data.Table)]
#: Initialization type
PCA, Random = 0, 1
#: Refresh rate
RefreshRate = [
("Every iteration", 1),
("Every 5 steps", 5),
("Every 10 steps", 10),
("Every 25 steps", 25),
("Every 50 steps", 50),
("None", -1)
]
JitterAmount = [
("None", 0),
("0.1 %", 0.1),
("0.5 %", 0.5),
("1 %", 1.0),
("2 %", 2.0)
]
#: Runtime state
Running, Finished, Waiting = 1, 2, 3
settingsHandler = settings.DomainContextHandler()
max_iter = settings.Setting(300)
initialization = settings.Setting(PCA)
refresh_rate = settings.Setting(3)
# output embedding role.
NoRole, AttrRole, AddAttrRole, MetaRole = 0, 1, 2, 3
output_embedding_role = settings.Setting(2)
autocommit = settings.Setting(True)
color_value = settings.ContextSetting("")
shape_value = settings.ContextSetting("")
size_value = settings.ContextSetting("")
label_value = settings.ContextSetting("")
label_only_selected = settings.Setting(False)
symbol_size = settings.Setting(8)
symbol_opacity = settings.Setting(230)
connected_pairs = settings.Setting(5)
jitter = settings.Setting(0)
legend_anchor = settings.Setting(((1, 0), (1, 0)))
graph_name = "plot.plotItem"
def __init__(self):
super().__init__()
self.matrix = None
self.data = None
self.subset_data = None # type: Optional[Orange.data.Table]
self.matrix_data = None
self.signal_data = None
self._pen_data = None
self._brush_data = None
self._shape_data = None
self._size_data = None
self._label_data = None
self._similar_pairs = None
self._scatter_item = None
self._legend_item = None
self._selection_mask = None
self._subset_mask = None # type: Optional[numpy.ndarray]
self._invalidated = False
self._effective_matrix = None
self.__update_loop = None
self.__state = OWMDS.Waiting
self.__in_next_step = False
self.__draw_similar_pairs = False
box = gui.vBox(self.controlArea, "MDS Optimization")
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
verticalSpacing=10
)
form.addRow("Max iterations:",
gui.spin(box, self, "max_iter", 10, 10 ** 4, step=1))
form.addRow("Initialization:",
gui.comboBox(box, self, "initialization",
items=["PCA (Torgerson)", "Random"],
callback=self.__invalidate_embedding))
box.layout().addLayout(form)
form.addRow("Refresh:",
gui.comboBox(
box, self, "refresh_rate",
items=[t for t, _ in OWMDS.RefreshRate],
callback=self.__invalidate_refresh))
gui.separator(box, 10)
self.runbutton = gui.button(
box, self, "Run", callback=self._toggle_run)
box = gui.vBox(self.controlArea, "Graph")
self.colorvar_model = itemmodels.VariableListModel()
common_options = dict(
sendSelectedValue=True, valueType=str, orientation=Qt.Horizontal,
labelWidth=50, contentsLength=12)
self.cb_color_value = gui.comboBox(
box, self, "color_value", label="Color:",
callback=self._on_color_index_changed, **common_options)
self.cb_color_value.setModel(self.colorvar_model)
self.shapevar_model = itemmodels.VariableListModel()
self.cb_shape_value = gui.comboBox(
box, self, "shape_value", label="Shape:",
callback=self._on_shape_index_changed, **common_options)
self.cb_shape_value.setModel(self.shapevar_model)
self.sizevar_model = itemmodels.VariableListModel()
self.cb_size_value = gui.comboBox(
box, self, "size_value", label="Size:",
callback=self._on_size_index_changed, **common_options)
self.cb_size_value.setModel(self.sizevar_model)
self.labelvar_model = itemmodels.VariableListModel()
self.cb_label_value = gui.comboBox(
box, self, "label_value", label="Label:",
callback=self._on_label_index_changed, **common_options)
self.cb_label_value.setModel(self.labelvar_model)
gui.checkBox(
gui.indentedBox(box), self, 'label_only_selected',
'Label only selected points', callback=self._on_label_index_changed)
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
verticalSpacing=10
)
form.addRow("Symbol size:",
gui.hSlider(box, self, "symbol_size",
minValue=1, maxValue=20,
callback=self._on_size_index_changed,
createLabel=False))
form.addRow("Symbol opacity:",
gui.hSlider(box, self, "symbol_opacity",
minValue=100, maxValue=255, step=100,
callback=self._on_color_index_changed,
createLabel=False))
form.addRow("Show similar pairs:",
gui.hSlider(
gui.hBox(self.controlArea),
self, "connected_pairs", minValue=0, maxValue=20,
createLabel=False,
callback=self._on_connected_changed))
form.addRow("Jitter:",
gui.comboBox(
box, self, "jitter",
items=[text for text, _ in self.JitterAmount],
callback=self._update_plot))
box.layout().addLayout(form)
gui.rubber(self.controlArea)
box = QtGui.QGroupBox("Zoom/Select", )
box.setLayout(QtGui.QHBoxLayout())
box.layout().setContentsMargins(2, 2, 2, 2)
group = QtGui.QActionGroup(self, exclusive=True)
def icon(name):
path = "icons/Dlg_{}.png".format(name)
path = pkg_resources.resource_filename(widget.__name__, path)
return QtGui.QIcon(path)
action_select = QtGui.QAction(
"Select", self, checkable=True, checked=True, icon=icon("arrow"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_1))
action_zoom = QtGui.QAction(
"Zoom", self, checkable=True, checked=False, icon=icon("zoom"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_2))
action_pan = QtGui.QAction(
"Pan", self, checkable=True, checked=False, icon=icon("pan_hand"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_3))
action_reset_zoom = QtGui.QAction(
"Zoom to fit", self, icon=icon("zoom_reset"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_0))
action_reset_zoom.triggered.connect(
lambda: self.plot.autoRange(padding=0.1,
items=[self._scatter_item]))
group.addAction(action_select)
group.addAction(action_zoom)
group.addAction(action_pan)
self.addActions(group.actions() + [action_reset_zoom])
action_select.setChecked(True)
def button(action):
b = QtGui.QToolButton()
b.setToolButtonStyle(Qt.ToolButtonIconOnly)
b.setDefaultAction(action)
return b
box.layout().addWidget(button(action_select))
box.layout().addWidget(button(action_zoom))
box.layout().addWidget(button(action_pan))
box.layout().addSpacing(4)
box.layout().addWidget(button(action_reset_zoom))
box.layout().addStretch()
self.controlArea.layout().addWidget(box)
box = gui.vBox(self.controlArea, "Output")
self.output_combo = gui.comboBox(
box, self, "output_embedding_role",
items=["Original features only",
"Coordinates only",
"Coordinates as features",
"Coordinates as meta attributes"],
callback=self._invalidate_output, addSpace=4)
gui.auto_commit(box, self, "autocommit", "Send Selected",
checkbox_label="Send selected automatically",
box=None)
self.plot = pg.PlotWidget(background="w", enableMenu=False)
self.plot.setAspectLocked(True)
self.plot.getPlotItem().hideAxis("bottom")
self.plot.getPlotItem().hideAxis("left")
self.plot.getPlotItem().hideButtons()
self.plot.setRenderHint(QtGui.QPainter.Antialiasing)
self.mainArea.layout().addWidget(self.plot)
self.selection_tool = PlotSelectionTool(parent=self)
self.zoom_tool = PlotZoomTool(parent=self)
self.pan_tool = PlotPanTool(parent=self)
self.pinch_tool = PlotPinchZoomTool(parent=self)
self.pinch_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.selectionFinished.connect(self.__selection_end)
self.current_tool = self.selection_tool
def activate_tool(action):
self.current_tool.setViewBox(None)
if action is action_select:
active, cur = self.selection_tool, Qt.ArrowCursor
elif action is action_zoom:
active, cur = self.zoom_tool, Qt.ArrowCursor
elif action is action_pan:
active, cur = self.pan_tool, Qt.OpenHandCursor
self.current_tool = active
self.current_tool.setViewBox(self.plot.getViewBox())
self.plot.getViewBox().setCursor(QtGui.QCursor(cur))
group.triggered[QtGui.QAction].connect(activate_tool)
self._initialize()
@check_sql_input
def set_data(self, data):
"""Set the input data set.
Parameters
----------
data : Optional[Orange.data.Table]
"""
self.signal_data = data
if self.matrix is not None and data is not None and len(self.matrix) == len(data):
self.closeContext()
self.data = data
self.update_controls()
self.openContext(data)
else:
self._invalidated = True
self._selection_mask = None
def set_disimilarity(self, matrix):
"""Set the dissimilarity (distance) matrix.
Parameters
----------
matrix : Optional[Orange.misc.DistMatrix]
"""
self.matrix = matrix
if matrix is not None and matrix.row_items:
self.matrix_data = matrix.row_items
if matrix is None:
self.matrix_data = None
self._invalidated = True
self._selection_mask = None
def set_subset_data(self, subset_data):
"""Set a subset of `data` input to highlight in the plot.
Parameters
----------
subset_data: Optional[Orange.data.Table]
"""
self.subset_data = subset_data
# invalidate the pen/brush when the subset is changed
self._pen_data = self._brush_data = None
self._subset_mask = None # type: Optional[numpy.ndarray]
def _clear(self):
self._pen_data = None
self._brush_data = None
self._shape_data = None
self._size_data = None
self._label_data = None
self._similar_pairs = None
self.colorvar_model[:] = ["Same color"]
self.shapevar_model[:] = ["Same shape"]
self.sizevar_model[:] = ["Same size"]
self.labelvar_model[:] = ["No labels"]
self.color_value = self.colorvar_model[0]
self.shape_value = self.shapevar_model[0]
self.size_value = self.sizevar_model[0]
self.label_value = self.labelvar_model[0]
self.__set_update_loop(None)
self.__state = OWMDS.Waiting
def _clear_plot(self):
self.plot.clear()
self._scatter_item = None
if self._legend_item is not None:
anchor = legend_anchor_pos(self._legend_item)
if anchor is not None:
self.legend_anchor = anchor
if self._legend_item.scene() is not None:
self._legend_item.scene().removeItem(self._legend_item)
self._legend_item = None
def update_controls(self):
if self.data is None and getattr(self.matrix, 'axis', 1) == 0:
# Column-wise distances
attr = "Attribute names"
self.labelvar_model[:] = ["No labels", attr]
self.shapevar_model[:] = ["Same shape", attr]
self.colorvar_model[:] = ["Same solor", attr]
self.color_value = attr
self.shape_value = attr
else:
# initialize the graph state from data
domain = self.data.domain
all_vars = list(filter_visible(domain.variables + domain.metas))
cd_vars = [var for var in all_vars if var.is_primitive()]
disc_vars = [var for var in all_vars if var.is_discrete]
cont_vars = [var for var in all_vars if var.is_continuous]
shape_vars = [var for var in disc_vars
if len(var.values) <= len(ScatterPlotItem.Symbols) - 1]
self.colorvar_model[:] = chain(["Same color"],
[self.colorvar_model.Separator] if cd_vars else [],
cd_vars)
self.shapevar_model[:] = chain(["Same shape"],
[self.shapevar_model.Separator] if shape_vars else [],
shape_vars)
self.sizevar_model[:] = chain(["Same size", "Stress"],
[self.sizevar_model.Separator] if cont_vars else [],
cont_vars)
self.labelvar_model[:] = chain(["No labels"],
[self.labelvar_model.Separator] if all_vars else [],
all_vars)
if domain.class_var is not None:
self.color_value = domain.class_var.name
def _initialize(self):
# clear everything
self.closeContext()
self._clear()
self.data = None
self._effective_matrix = None
self.embedding = None
# if no data nor matrix is present reset plot
if self.signal_data is None and self.matrix is None:
return
if self.signal_data and self.matrix is not None and len(self.signal_data) != len(self.matrix):
self.error(1, "Data and distances dimensions do not match.")
self._update_plot()
return
self.error(1)
if self.signal_data:
self.data = self.signal_data
elif self.matrix_data:
self.data = self.matrix_data
if self.matrix is not None:
self._effective_matrix = self.matrix
if self.matrix.axis == 0 and self.data is self.matrix_data:
self.data = None
else:
preprocessed_data = Orange.projection.MDS().preprocess(self.data)
self._effective_matrix = Orange.distance.Euclidean(preprocessed_data)
self.update_controls()
self.openContext(self.data)
def _toggle_run(self):
if self.__state == OWMDS.Running:
self.stop()
self._invalidate_output()
else:
self.start()
def start(self):
if self.__state == OWMDS.Running:
return
elif self.__state == OWMDS.Finished:
# Resume/continue from a previous run
self.__start()
elif self.__state == OWMDS.Waiting and \
self._effective_matrix is not None:
self.__start()
def stop(self):
if self.__state == OWMDS.Running:
self.__set_update_loop(None)
def __start(self):
self.__draw_similar_pairs = False
X = self._effective_matrix
if self.embedding is not None:
init = self.embedding
elif self.initialization == OWMDS.PCA:
init = torgerson(X, n_components=2)
else:
init = None
# number of iterations per single GUI update step
_, step_size = OWMDS.RefreshRate[self.refresh_rate]
if step_size == -1:
step_size = self.max_iter
def update_loop(X, max_iter, step, init):
"""
return an iterator over successive improved MDS point embeddings.
"""
# NOTE: this code MUST NOT call into QApplication.processEvents
done = False
iterations_done = 0
oldstress = numpy.finfo(numpy.float).max
while not done:
step_iter = min(max_iter - iterations_done, step)
mds = Orange.projection.MDS(
dissimilarity="precomputed", n_components=2,
n_init=1, max_iter=step_iter)
mdsfit = mds.fit(X, init=init)
iterations_done += step_iter
embedding, stress = mdsfit.embedding_, mdsfit.stress_
stress /= numpy.sqrt(numpy.sum(embedding ** 2, axis=1)).sum()
if iterations_done >= max_iter:
done = True
elif (oldstress - stress) < mds.params["eps"]:
done = True
init = embedding
oldstress = stress
yield embedding, mdsfit.stress_, iterations_done / max_iter
self.__set_update_loop(update_loop(X, self.max_iter, step_size, init))
self.progressBarInit(processEvents=None)
def __set_update_loop(self, loop):
"""
Set the update `loop` coroutine.
The `loop` is a generator yielding `(embedding, stress, progress)`
tuples where `embedding` is a `(N, 2) ndarray` of current updated
MDS points, `stress` is the current stress and `progress` a float
ratio (0 <= progress <= 1)
If an existing update loop is already in palace it is interrupted
(closed).
.. note::
The `loop` must not explicitly yield control flow to the event
loop (i.e. call `QApplication.processEvents`)
"""
if self.__update_loop is not None:
self.__update_loop.close()
self.__update_loop = None
self.progressBarFinished(processEvents=None)
self.__update_loop = loop
if loop is not None:
self.progressBarInit(processEvents=None)
self.setStatusMessage("Running")
self.runbutton.setText("Stop")
self.__state = OWMDS.Running
QtGui.QApplication.postEvent(self, QEvent(QEvent.User))
else:
self.setStatusMessage("")
self.runbutton.setText("Start")
self.__state = OWMDS.Finished
def __next_step(self):
if self.__update_loop is None:
return
loop = self.__update_loop
try:
embedding, stress, progress = next(self.__update_loop)
assert self.__update_loop is loop
except StopIteration:
self.__set_update_loop(None)
self.unconditional_commit()
self.__draw_similar_pairs = True
self._update_plot()
self.plot.autoRange(padding=0.1, items=[self._scatter_item])
else:
self.progressBarSet(100.0 * progress, processEvents=None)
self.embedding = embedding
self._update_plot()
self.plot.autoRange(padding=0.1, items=[self._scatter_item])
# schedule next update
QtGui.QApplication.postEvent(
self, QEvent(QEvent.User), Qt.LowEventPriority)
def customEvent(self, event):
if event.type() == QEvent.User and self.__update_loop is not None:
if not self.__in_next_step:
self.__in_next_step = True
try:
self.__next_step()
finally:
self.__in_next_step = False
else:
warnings.warn(
"Re-entry in update loop detected. "
"A rogue `proccessEvents` is on the loose.",
RuntimeWarning)
# re-schedule the update iteration.
QtGui.QApplication.postEvent(self, QEvent(QEvent.User))
return super().customEvent(event)
def __invalidate_embedding(self):
# reset/invalidate the MDS embedding, to the default initialization
# (Random or PCA), restarting the optimization if necessary.
if self.embedding is None:
return
state = self.__state
if self.__update_loop is not None:
self.__set_update_loop(None)
X = self._effective_matrix
if self.initialization == OWMDS.PCA:
self.embedding = torgerson(X)
else:
self.embedding = numpy.random.rand(len(X), 2)
self._update_plot()
self.plot.autoRange(padding=0.1, items=[self._scatter_item])
# restart the optimization if it was interrupted.
if state == OWMDS.Running:
self.__start()
def __invalidate_refresh(self):
state = self.__state
if self.__update_loop is not None:
self.__set_update_loop(None)
# restart the optimization if it was interrupted.
# TODO: decrease the max iteration count by the already
# completed iterations count.
if state == OWMDS.Running:
self.__start()
def handleNewSignals(self):
if self._invalidated:
self._invalidated = False
self._initialize()
self.start()
self.__draw_similar_pairs = False
if self._subset_mask is None and self.subset_data is not None and \
self.data is not None:
self._subset_mask = numpy.in1d(self.data.ids, self.subset_data.ids)
self._update_plot()
self.plot.autoRange(padding=0.1)
self.unconditional_commit()
def _invalidate_output(self):
self.commit()
def _on_color_index_changed(self):
self._pen_data = None
self._update_plot()
def _on_shape_index_changed(self):
self._shape_data = None
self._update_plot()
def _on_size_index_changed(self):
self._size_data = None
self._update_plot()
def _on_label_index_changed(self):
self._label_data = None
self._update_plot()
def _on_connected_changed(self):
self._similar_pairs = None
self._update_plot()
def _update_plot(self):
self._clear_plot()
if self.embedding is not None:
self._setup_plot()
def _setup_plot(self):
have_data = self.data is not None
have_matrix_transposed = self.matrix is not None and not self.matrix.axis
plotstyle = mdsplotutils.plotstyle
size = self._effective_matrix.shape[0]
def column(data, variable):
a, _ = data.get_column_view(variable)
return a.ravel()
def attributes(matrix):
return matrix.row_items.domain.attributes
def scale(a):
dmin, dmax = numpy.nanmin(a), numpy.nanmax(a)
if dmax - dmin > 0:
return (a - dmin) / (dmax - dmin)
else:
return numpy.zeros_like(a)
def jitter(x, factor=1, rstate=None):
if rstate is None:
rstate = numpy.random.RandomState()
elif not isinstance(rstate, numpy.random.RandomState):
rstate = numpy.random.RandomState(rstate)
span = numpy.nanmax(x) - numpy.nanmin(x)
if span < numpy.finfo(x.dtype).eps * 100:
span = 1
a = factor * span / 100.
return x + (rstate.random_sample(x.shape) - 0.5) * a
if self._pen_data is None:
if self._selection_mask is not None:
pointflags = numpy.where(
self._selection_mask,
mdsplotutils.Selected, mdsplotutils.NoFlags)
else:
pointflags = None
color_index = self.cb_color_value.currentIndex()
if have_data and color_index > 0:
color_var = self.colorvar_model[color_index]
if color_var.is_discrete:
palette = colorpalette.ColorPaletteGenerator(
len(color_var.values)
)
plotstyle = plotstyle.updated(discrete_palette=palette)
else:
palette = None
color_data = mdsplotutils.color_data(
self.data, color_var, plotstyle=plotstyle)
color_data = numpy.hstack(
(color_data,
numpy.full((len(color_data), 1), self.symbol_opacity,
dtype=float))
)
pen_data = mdsplotutils.pen_data(color_data * 0.8, pointflags)
brush_data = mdsplotutils.brush_data(color_data)
elif have_matrix_transposed and \
self.colorvar_model[color_index] == 'Attribute names':
attr = attributes(self.matrix)
palette = colorpalette.ColorPaletteGenerator(len(attr))
color_data = [palette.getRGB(i) for i in range(len(attr))]
color_data = numpy.hstack((
color_data,
numpy.full((len(color_data), 1), self.symbol_opacity,
dtype=float))
)
pen_data = mdsplotutils.pen_data(color_data * 0.8, pointflags)
brush_data = mdsplotutils.brush_data(color_data)
else:
pen_data = make_pen(QtGui.QColor(Qt.darkGray), cosmetic=True)
if self._selection_mask is not None:
pen_data = numpy.array(
[pen_data, plotstyle.selected_pen])
pen_data = pen_data[self._selection_mask.astype(int)]
else:
pen_data = numpy.full(self._effective_matrix.dim, pen_data,
dtype=object)
brush_data = numpy.full(
size, pg.mkColor((192, 192, 192, self.symbol_opacity)),
dtype=object)
if self._subset_mask is not None and have_data and \
self._subset_mask.shape == (size, ):
# clear brush fill for non subset data
brush_data[~self._subset_mask] = QtGui.QBrush(Qt.NoBrush)
self._pen_data = pen_data
self._brush_data = brush_data
if self._shape_data is None:
shape_index = self.cb_shape_value.currentIndex()
if have_data and shape_index > 0:
Symbols = ScatterPlotItem.Symbols
symbols = numpy.array(list(Symbols.keys()))
shape_var = self.shapevar_model[shape_index]
data = column(self.data, shape_var).astype(numpy.float)
data = data % (len(Symbols) - 1)
data[numpy.isnan(data)] = len(Symbols) - 1
shape_data = symbols[data.astype(int)]
elif have_matrix_transposed and \
self.shapevar_model[shape_index] == 'Attribute names':
Symbols = ScatterPlotItem.Symbols
symbols = numpy.array(list(Symbols.keys()))
attr = [i % (len(Symbols) - 1)
for i, _ in enumerate(attributes(self.matrix))]
shape_data = symbols[attr]
else:
shape_data = "o"
self._shape_data = shape_data
if self._size_data is None:
MinPointSize = 3
point_size = self.symbol_size + MinPointSize
size_index = self.cb_size_value.currentIndex()
if have_data and size_index == 1:
# size by stress
size_data = stress(self.embedding, self._effective_matrix)
size_data = scale(size_data)
size_data = MinPointSize + size_data * point_size
elif have_data and size_index > 0:
size_var = self.sizevar_model[size_index]
size_data = column(self.data, size_var)
size_data = scale(size_data)
size_data = MinPointSize + size_data * point_size
else:
size_data = point_size
self._size_data = size_data
if self._label_data is None:
label_index = self.cb_label_value.currentIndex()
if have_data and label_index > 0:
label_var = self.labelvar_model[label_index]
label_data = column(self.data, label_var)
label_data = [label_var.str_val(val) for val in label_data]
label_items = [pg.TextItem(text, anchor=(0.5, 0), color=0.0)
for text in label_data]
elif have_matrix_transposed and \
self.labelvar_model[label_index] == 'Attribute names':
attr = attributes(self.matrix)
label_items = [pg.TextItem(str(text), anchor=(0.5, 0))
for text in attr]
else:
label_items = None
self._label_data = label_items
emb_x, emb_y = self.embedding[:, 0], self.embedding[:, 1]
if self.jitter > 0:
_, jitter_factor = self.JitterAmount[self.jitter]
emb_x = jitter(emb_x, jitter_factor, rstate=42)
emb_y = jitter(emb_y, jitter_factor, rstate=667)
if self.connected_pairs and self.__draw_similar_pairs:
if self._similar_pairs is None:
# This code requires storing lower triangle of X (n x n / 2
# doubles), n x n / 2 * 2 indices to X, n x n / 2 indices for
# argsort result. If this becomes an issue, it can be reduced to
# n x n argsort indices by argsorting the entire X. Then we
# take the first n + 2 * p indices. We compute their coordinates
# i, j in the original matrix. We keep those for which i < j.
# n + 2 * p will suffice to exclude the diagonal (i = j). If the
# number of those for which i < j is smaller than p, we instead
# take i > j. Among those that remain, we take the first p.
# Assuming that MDS can't show so many points that memory could
# become an issue, I preferred using simpler code.
m = self._effective_matrix
n = len(m)
p = (n * (n - 1) // 2 * self.connected_pairs) // 100
indcs = numpy.triu_indices(n, 1)
sorted = numpy.argsort(m[indcs])[:p]
self._similar_pairs = fpairs = numpy.empty(2 * p, dtype=int)
fpairs[::2] = indcs[0][sorted]
fpairs[1::2] = indcs[1][sorted]
for i in range(int(len(emb_x[self._similar_pairs]) / 2)):
item = QtGui.QGraphicsLineItem(
emb_x[self._similar_pairs][i * 2],
emb_y[self._similar_pairs][i * 2],
emb_x[self._similar_pairs][i * 2 + 1],
emb_y[self._similar_pairs][i * 2 + 1]
)
pen = QtGui.QPen(QtGui.QBrush(QtGui.QColor(204, 204, 204)), 2)
pen.setCosmetic(True)
item.setPen(pen)
self.plot.addItem(item)
data = numpy.arange(size)
self._scatter_item = item = ScatterPlotItem(
x=emb_x, y=emb_y,
pen=self._pen_data, brush=self._brush_data, symbol=self._shape_data,
size=self._size_data, data=data,
antialias=True
)
self.plot.addItem(item)
if self._label_data is not None:
if self.label_only_selected:
if self._selection_mask is not None:
for (x, y), text_item, selected \
in zip(self.embedding, self._label_data,
self._selection_mask):
if selected:
self.plot.addItem(text_item)
text_item.setPos(x, y)
else:
for (x, y), text_item in zip(self.embedding, self._label_data):
self.plot.addItem(text_item)
text_item.setPos(x, y)
self._legend_item = LegendItem()
viewbox = self.plot.getViewBox()
self._legend_item.setParentItem(self.plot.getViewBox())
self._legend_item.setZValue(viewbox.zValue() + 10)
self._legend_item.restoreAnchor(self.legend_anchor)
color_var = shape_var = None
color_index = self.cb_color_value.currentIndex()
if have_data and 1 <= color_index < len(self.colorvar_model):
color_var = self.colorvar_model[color_index]
assert isinstance(color_var, Orange.data.Variable)
shape_index = self.cb_shape_value.currentIndex()
if have_data and 1 <= shape_index < len(self.shapevar_model):
shape_var = self.shapevar_model[shape_index]
assert isinstance(shape_var, Orange.data.Variable)
if shape_var is not None or \
(color_var is not None and color_var.is_discrete):
legend_data = mdsplotutils.legend_data(
color_var, shape_var, plotstyle=plotstyle)
for color, symbol, text in legend_data:
self._legend_item.addItem(
ScatterPlotItem(pen=color, brush=color, symbol=symbol,
size=10),
escape(text)
)
else:
self._legend_item.hide()
def commit(self):
if self.embedding is not None:
output = embedding = Orange.data.Table.from_numpy(
Orange.data.Domain([Orange.data.ContinuousVariable("X"),
Orange.data.ContinuousVariable("Y")]),
self.embedding
)
else:
output = embedding = None
if self.embedding is not None and self.data is not None:
domain = self.data.domain
attrs = domain.attributes
class_vars = domain.class_vars
metas = domain.metas
if self.output_embedding_role == OWMDS.AttrRole:
attrs = embedding.domain.attributes
elif self.output_embedding_role == OWMDS.AddAttrRole:
attrs = domain.attributes + embedding.domain.attributes
elif self.output_embedding_role == OWMDS.MetaRole:
metas += embedding.domain.attributes
domain = Orange.data.Domain(attrs, class_vars, metas)
output = Orange.data.Table.from_table(domain, self.data)
if self.output_embedding_role == OWMDS.AttrRole:
output.X[:] = embedding.X
if self.output_embedding_role == OWMDS.AddAttrRole:
output.X[:, -2:] = embedding.X
elif self.output_embedding_role == OWMDS.MetaRole:
output.metas[:, -2:] = embedding.X
self.send("Data", output)
if output is not None and self._selection_mask is not None and \
numpy.any(self._selection_mask):
subset = output[self._selection_mask]
else:
subset = None
self.send("Selected Data", subset)
def onDeleteWidget(self):
super().onDeleteWidget()
self._clear_plot()
self._clear()
def __selection_end(self, path):
self.select(path)
self._pen_data = None
self._update_plot()
self._invalidate_output()
def select(self, region):
item = self._scatter_item
if item is None:
return
indices = numpy.array(
[spot.data() for spot in item.points()
if region.contains(spot.pos())],
dtype=int)
if not QtGui.QApplication.keyboardModifiers():
self._selection_mask = None
self.select_indices(indices, QtGui.QApplication.keyboardModifiers())
def select_indices(self, indices, modifiers=Qt.NoModifier):
if self.data is None:
return
if self._selection_mask is None or \
not modifiers & (Qt.ControlModifier | Qt.ShiftModifier |
Qt.AltModifier):
self._selection_mask = numpy.zeros(len(self.data), dtype=bool)
if modifiers & Qt.AltModifier:
self._selection_mask[indices] = False
elif modifiers & Qt.ControlModifier:
self._selection_mask[indices] = ~self._selection_mask[indices]
else:
self._selection_mask[indices] = True
def send_report(self):
if self.data is None:
return
self.report_plot()
caption = report.render_items_vert((
("Color", self.color_value != "Same color" and self.color_value),
("Shape", self.shape_value != "Same shape" and self.shape_value),
("Size", self.size_value != "Same size" and self.size_value),
("Labels", self.label_value != "No labels" and self.label_value)))
if caption:
self.report_caption(caption)
self.report_items((("Output", self.output_combo.currentText()),))
def __init__(self):
super().__init__()
self.matrix = None
self.data = None
self.subset_data = None # type: Optional[Orange.data.Table]
self.matrix_data = None
self.signal_data = None
self._pen_data = None
self._brush_data = None
self._shape_data = None
self._size_data = None
self._label_data = None
self._similar_pairs = None
self._scatter_item = None
self._legend_item = None
self._selection_mask = None
self._subset_mask = None # type: Optional[numpy.ndarray]
self._invalidated = False
self._effective_matrix = None
self.__update_loop = None
self.__state = OWMDS.Waiting
self.__in_next_step = False
self.__draw_similar_pairs = False
box = gui.vBox(self.controlArea, "MDS Optimization")
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
verticalSpacing=10
)
form.addRow("Max iterations:",
gui.spin(box, self, "max_iter", 10, 10 ** 4, step=1))
form.addRow("Initialization:",
gui.comboBox(box, self, "initialization",
items=["PCA (Torgerson)", "Random"],
callback=self.__invalidate_embedding))
box.layout().addLayout(form)
form.addRow("Refresh:",
gui.comboBox(
box, self, "refresh_rate",
items=[t for t, _ in OWMDS.RefreshRate],
callback=self.__invalidate_refresh))
gui.separator(box, 10)
self.runbutton = gui.button(
box, self, "Run", callback=self._toggle_run)
box = gui.vBox(self.controlArea, "Graph")
self.colorvar_model = itemmodels.VariableListModel()
common_options = dict(
sendSelectedValue=True, valueType=str, orientation=Qt.Horizontal,
labelWidth=50, contentsLength=12)
self.cb_color_value = gui.comboBox(
box, self, "color_value", label="Color:",
callback=self._on_color_index_changed, **common_options)
self.cb_color_value.setModel(self.colorvar_model)
self.shapevar_model = itemmodels.VariableListModel()
self.cb_shape_value = gui.comboBox(
box, self, "shape_value", label="Shape:",
callback=self._on_shape_index_changed, **common_options)
self.cb_shape_value.setModel(self.shapevar_model)
self.sizevar_model = itemmodels.VariableListModel()
self.cb_size_value = gui.comboBox(
box, self, "size_value", label="Size:",
callback=self._on_size_index_changed, **common_options)
self.cb_size_value.setModel(self.sizevar_model)
self.labelvar_model = itemmodels.VariableListModel()
self.cb_label_value = gui.comboBox(
box, self, "label_value", label="Label:",
callback=self._on_label_index_changed, **common_options)
self.cb_label_value.setModel(self.labelvar_model)
gui.checkBox(
gui.indentedBox(box), self, 'label_only_selected',
'Label only selected points', callback=self._on_label_index_changed)
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
verticalSpacing=10
)
form.addRow("Symbol size:",
gui.hSlider(box, self, "symbol_size",
minValue=1, maxValue=20,
callback=self._on_size_index_changed,
createLabel=False))
form.addRow("Symbol opacity:",
gui.hSlider(box, self, "symbol_opacity",
minValue=100, maxValue=255, step=100,
callback=self._on_color_index_changed,
createLabel=False))
form.addRow("Show similar pairs:",
gui.hSlider(
gui.hBox(self.controlArea),
self, "connected_pairs", minValue=0, maxValue=20,
createLabel=False,
callback=self._on_connected_changed))
form.addRow("Jitter:",
gui.comboBox(
box, self, "jitter",
items=[text for text, _ in self.JitterAmount],
callback=self._update_plot))
box.layout().addLayout(form)
gui.rubber(self.controlArea)
box = QtGui.QGroupBox("Zoom/Select", )
box.setLayout(QtGui.QHBoxLayout())
box.layout().setContentsMargins(2, 2, 2, 2)
group = QtGui.QActionGroup(self, exclusive=True)
def icon(name):
path = "icons/Dlg_{}.png".format(name)
path = pkg_resources.resource_filename(widget.__name__, path)
return QtGui.QIcon(path)
action_select = QtGui.QAction(
"Select", self, checkable=True, checked=True, icon=icon("arrow"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_1))
action_zoom = QtGui.QAction(
"Zoom", self, checkable=True, checked=False, icon=icon("zoom"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_2))
action_pan = QtGui.QAction(
"Pan", self, checkable=True, checked=False, icon=icon("pan_hand"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_3))
action_reset_zoom = QtGui.QAction(
"Zoom to fit", self, icon=icon("zoom_reset"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_0))
action_reset_zoom.triggered.connect(
lambda: self.plot.autoRange(padding=0.1,
items=[self._scatter_item]))
group.addAction(action_select)
group.addAction(action_zoom)
group.addAction(action_pan)
self.addActions(group.actions() + [action_reset_zoom])
action_select.setChecked(True)
def button(action):
b = QtGui.QToolButton()
b.setToolButtonStyle(Qt.ToolButtonIconOnly)
b.setDefaultAction(action)
return b
box.layout().addWidget(button(action_select))
box.layout().addWidget(button(action_zoom))
box.layout().addWidget(button(action_pan))
box.layout().addSpacing(4)
box.layout().addWidget(button(action_reset_zoom))
box.layout().addStretch()
self.controlArea.layout().addWidget(box)
box = gui.vBox(self.controlArea, "Output")
self.output_combo = gui.comboBox(
box, self, "output_embedding_role",
items=["Original features only",
"Coordinates only",
"Coordinates as features",
"Coordinates as meta attributes"],
callback=self._invalidate_output, addSpace=4)
gui.auto_commit(box, self, "autocommit", "Send Selected",
checkbox_label="Send selected automatically",
box=None)
self.plot = pg.PlotWidget(background="w", enableMenu=False)
self.plot.setAspectLocked(True)
self.plot.getPlotItem().hideAxis("bottom")
self.plot.getPlotItem().hideAxis("left")
self.plot.getPlotItem().hideButtons()
self.plot.setRenderHint(QtGui.QPainter.Antialiasing)
self.mainArea.layout().addWidget(self.plot)
self.selection_tool = PlotSelectionTool(parent=self)
self.zoom_tool = PlotZoomTool(parent=self)
self.pan_tool = PlotPanTool(parent=self)
self.pinch_tool = PlotPinchZoomTool(parent=self)
self.pinch_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.selectionFinished.connect(self.__selection_end)
self.current_tool = self.selection_tool
def activate_tool(action):
self.current_tool.setViewBox(None)
if action is action_select:
active, cur = self.selection_tool, Qt.ArrowCursor
elif action is action_zoom:
active, cur = self.zoom_tool, Qt.ArrowCursor
elif action is action_pan:
active, cur = self.pan_tool, Qt.OpenHandCursor
self.current_tool = active
self.current_tool.setViewBox(self.plot.getViewBox())
self.plot.getViewBox().setCursor(QtGui.QCursor(cur))
group.triggered[QtGui.QAction].connect(activate_tool)
self._initialize()
class OWMDS(widget.OWWidget):
name = "MDS"
description = "Two-dimensional data projection by multidimensional " \
"scaling constructed from a distance matrix."
icon = "icons/MDS.svg"
inputs = [("Data", Orange.data.Table, "set_data"),
("Distances", Orange.misc.DistMatrix, "set_disimilarity")]
outputs = [("Data", Orange.data.Table, widget.Default),
("Data Subset", Orange.data.Table)]
#: Initialization type
PCA, Random = 0, 1
#: Refresh rate
RefreshRate = [("Every iteration", 1), ("Every 5 steps", 5),
("Every 10 steps", 10), ("Every 25 steps", 25),
("Every 50 steps", 50), ("None", -1)]
#: Runtime state
Running, Finished, Waiting = 1, 2, 3
settingsHandler = settings.DomainContextHandler()
max_iter = settings.Setting(300)
initialization = settings.Setting(PCA)
refresh_rate = settings.Setting(3)
# output embedding role.
NoRole, AttrRole, MetaRole = 0, 1, 2
output_embedding_role = settings.Setting(1)
autocommit = settings.Setting(True)
color_index = settings.ContextSetting(0, not_attribute=True)
shape_index = settings.ContextSetting(0, not_attribute=True)
size_index = settings.ContextSetting(0, not_attribute=True)
label_index = settings.ContextSetting(0, not_attribute=True)
symbol_size = settings.Setting(8)
symbol_opacity = settings.Setting(230)
def __init__(self, parent=None):
super().__init__(parent)
self.matrix = None
self.data = None
self.matrix_data = None
self.signal_data = None
self._pen_data = None
self._shape_data = None
self._size_data = None
self._label_data = None
self._scatter_item = None
self._selection_item = None
self._selection_mask = None
self._invalidated = False
self._effective_matrix = None
self.__update_loop = None
self.__state = OWMDS.Waiting
self.__in_next_step = False
box = gui.widgetBox(self.controlArea, "MDS Optimization")
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
)
form.addRow("Max iterations:",
gui.spin(box, self, "max_iter", 10, 10**4, step=1))
form.addRow(
"Initialization",
gui.comboBox(box,
self,
"initialization",
items=["PCA (Torgerson)", "Random"],
callback=self.__invalidate_embedding))
box.layout().addLayout(form)
form.addRow(
"Refresh",
gui.comboBox(box,
self,
"refresh_rate",
items=[t for t, _ in OWMDS.RefreshRate],
callback=self.__invalidate_refresh))
self.runbutton = gui.button(box,
self,
"Run",
callback=self._toggle_run)
box = gui.widgetBox(self.controlArea, "Graph")
self.colorvar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box,
self,
"color_index",
box="Color",
callback=self._on_color_index_changed)
cb.setModel(self.colorvar_model)
cb.box.setFlat(True)
self.shapevar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box,
self,
"shape_index",
box="Shape",
callback=self._on_shape_index_changed)
cb.setModel(self.shapevar_model)
cb.box.setFlat(True)
self.sizevar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box,
self,
"size_index",
"Size",
callback=self._on_size_index_changed)
cb.setModel(self.sizevar_model)
cb.box.setFlat(True)
self.labelvar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box,
self,
"label_index",
"Label",
callback=self._on_label_index_changed)
cb.setModel(self.labelvar_model)
cb.box.setFlat(True)
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
)
form.addRow(
"Symbol size",
gui.hSlider(box,
self,
"symbol_size",
minValue=1,
maxValue=20,
callback=self._on_size_index_changed,
createLabel=False))
form.addRow(
"Symbol opacity",
gui.hSlider(box,
self,
"symbol_opacity",
minValue=100,
maxValue=255,
step=100,
callback=self._on_color_index_changed,
createLabel=False))
box.layout().addLayout(form)
box = QtGui.QGroupBox("Zoom/Select", )
box.setLayout(QtGui.QHBoxLayout())
group = QtGui.QActionGroup(self, exclusive=True)
def icon(name):
path = "icons/Dlg_{}.png".format(name)
path = pkg_resources.resource_filename(widget.__name__, path)
return QtGui.QIcon(path)
action_select = QtGui.QAction(
"Select",
self,
checkable=True,
checked=True,
icon=icon("arrow"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_1))
action_zoom = QtGui.QAction(
"Zoom",
self,
checkable=True,
checked=False,
icon=icon("zoom"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_2))
action_pan = QtGui.QAction(
"Pan",
self,
checkable=True,
checked=False,
icon=icon("pan_hand"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_3))
action_reset_zoom = QtGui.QAction(
"Zoom to fit",
self,
icon=icon("zoom_reset"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_0))
action_reset_zoom.triggered.connect(lambda: self.plot.autoRange())
group.addAction(action_select)
group.addAction(action_zoom)
group.addAction(action_pan)
self.addActions(group.actions() + [action_reset_zoom])
action_select.setChecked(True)
def button(action):
b = QtGui.QToolButton()
b.setToolButtonStyle(Qt.ToolButtonIconOnly)
b.setDefaultAction(action)
return b
box.layout().addWidget(button(action_select))
box.layout().addWidget(button(action_zoom))
box.layout().addWidget(button(action_pan))
box.layout().addSpacing(4)
box.layout().addWidget(button(action_reset_zoom))
box.layout().addStretch()
self.controlArea.layout().addWidget(box)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, "Output")
cb = gui.comboBox(box,
self,
"output_embedding_role",
box="Append coordinates",
items=["Do not append", "As attributes", "As metas"],
callback=self._invalidate_output)
cb.box.setFlat(True)
gui.auto_commit(box,
self,
"autocommit",
"Send data",
checkbox_label="Send after any change",
box=None)
self.plot = pg.PlotWidget(background="w", enableMenu=False)
self.mainArea.layout().addWidget(self.plot)
self.selection_tool = PlotSelectionTool(
parent=self, selectionMode=PlotSelectionTool.Lasso)
self.zoom_tool = PlotZoomTool(parent=self)
self.pan_tool = PlotPanTool(parent=self)
self.pinch_tool = PlotPinchZoomTool(parent=self)
self.pinch_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.selectionFinished.connect(self.__selection_end)
self.current_tool = self.selection_tool
def activate_tool(action):
self.current_tool.setViewBox(None)
if action is action_select:
active, cur = self.selection_tool, Qt.ArrowCursor
elif action is action_zoom:
active, cur = self.zoom_tool, Qt.ArrowCursor
elif action is action_pan:
active, cur = self.pan_tool, Qt.OpenHandCursor
self.current_tool = active
self.current_tool.setViewBox(self.plot.getViewBox())
self.plot.getViewBox().setCursor(QtGui.QCursor(cur))
group.triggered[QtGui.QAction].connect(activate_tool)
def set_data(self, data):
self.signal_data = data
if self.matrix and data is not None and len(
self.matrix.X) == len(data):
self.closeContext()
self.data = data
self.update_controls()
self.openContext(data)
else:
self._invalidated = True
self._selection_mask = None
def set_disimilarity(self, matrix):
self.matrix = matrix
if matrix and matrix.row_items:
self.matrix_data = matrix.row_items
if matrix is None:
self.matrix_data = None
self._invalidated = True
self._selection_mask = None
def _clear(self):
self._pen_data = None
self._shape_data = None
self._size_data = None
self._label_data = None
self.colorvar_model[:] = ["Same color"]
self.shapevar_model[:] = ["Same shape"]
self.sizevar_model[:] = ["Same size"]
self.labelvar_model[:] = ["No labels"]
self.color_index = 0
self.shape_index = 0
self.size_index = 0
self.label_index = 0
self.__set_update_loop(None)
self.__state = OWMDS.Waiting
def update_controls(self):
if getattr(self.matrix, 'axis', 1) == 0:
# Column-wise distances
attr = "Attribute names"
self.labelvar_model[:] = ["No labels", attr]
self.shapevar_model[:] = ["Same shape", attr]
self.colorvar_model[:] = ["Same color", attr]
self.color_index = list(self.colorvar_model).index(attr)
self.shape_index = list(self.shapevar_model).index(attr)
else:
# initialize the graph state from data
domain = self.data.domain
all_vars = list(domain.variables + domain.metas)
cd_vars = [var for var in all_vars if var.is_primitive()]
disc_vars = [var for var in all_vars if var.is_discrete]
cont_vars = [var for var in all_vars if var.is_continuous]
str_vars = [
var for var in all_vars if var.is_discrete or var.is_string
]
def set_separator(model, index):
index = model.index(index, 0)
model.setData(index, "separator", Qt.AccessibleDescriptionRole)
model.setData(index, Qt.NoItemFlags, role="flags")
self.colorvar_model[:] = ["Same color", ""] + cd_vars
set_separator(self.colorvar_model, 1)
self.shapevar_model[:] = ["Same shape", ""] + disc_vars
set_separator(self.shapevar_model, 1)
self.sizevar_model[:] = ["Same size", "Stress", ""] + cont_vars
set_separator(self.sizevar_model, 2)
self.labelvar_model[:] = ["No labels", ""] + str_vars
set_separator(self.labelvar_model, 1)
if domain.class_var is not None:
self.color_index = list(self.colorvar_model).index(
domain.class_var)
def _initialize(self):
# clear everything
self.closeContext()
self._clear()
self.data = None
self._effective_matrix = None
self.embedding = None
# if no data nor matrix is present reset plot
if self.signal_data is None and self.matrix is None:
self._update_plot()
return
if self.signal_data and self.matrix_data and len(
self.signal_data) != len(self.matrix_data):
self.error(1, "Data and distances dimensions do not match.")
self._update_plot()
return
self.error(1)
if self.signal_data:
self.data = self.signal_data
elif self.matrix_data:
self.data = self.matrix_data
if self.matrix:
self._effective_matrix = self.matrix
if self.matrix.axis == 0:
self.data = None
else:
self._effective_matrix = Orange.distance.Euclidean(self.data)
self.update_controls()
self.openContext(self.data)
def _toggle_run(self):
if self.__state == OWMDS.Running:
self.stop()
self._invalidate_output()
else:
self.start()
def start(self):
if self.__state == OWMDS.Running:
return
elif self.__state == OWMDS.Finished:
# Resume/continue from a previous run
self.__start()
elif self.__state == OWMDS.Waiting and \
self._effective_matrix is not None:
self.__start()
def stop(self):
if self.__state == OWMDS.Running:
self.__set_update_loop(None)
def __start(self):
X = self._effective_matrix.X
if self.embedding is not None:
init = self.embedding
elif self.initialization == OWMDS.PCA:
init = torgerson(X, n_components=2)
else:
init = None
# number of iterations per single GUI update step
_, step_size = OWMDS.RefreshRate[self.refresh_rate]
if step_size == -1:
step_size = self.max_iter
def update_loop(X, max_iter, step, init):
"""
return an iterator over successive improved MDS point embeddings.
"""
# NOTE: this code MUST NOT call into QApplication.processEvents
done = False
iterations_done = 0
oldstress = numpy.finfo(numpy.float).max
while not done:
step_iter = min(max_iter - iterations_done, step)
mds = Orange.projection.MDS(dissimilarity="precomputed",
n_components=2,
n_init=1,
max_iter=step_iter)
mdsfit = mds.fit(X, init=init)
iterations_done += step_iter
embedding, stress = mdsfit.embedding_, mdsfit.stress_
stress /= numpy.sqrt(numpy.sum(embedding**2, axis=1)).sum()
if iterations_done >= max_iter:
done = True
elif (oldstress - stress) < mds.params["eps"]:
done = True
init = embedding
oldstress = stress
yield embedding, mdsfit.stress_, iterations_done / max_iter
self.__set_update_loop(update_loop(X, self.max_iter, step_size, init))
self.progressBarInit(processEvents=None)
def __set_update_loop(self, loop):
"""
Set the update `loop` coroutine.
The `loop` is a generator yielding `(embedding, stress, progress)`
tuples where `embedding` is a `(N, 2) ndarray` of current updated
MDS points, `stress` is the current stress and `progress` a float
ratio (0 <= progress <= 1)
If an existing update loop is already in palace it is interrupted
(closed).
.. note::
The `loop` must not explicitly yield control flow to the event
loop (i.e. call `QApplication.proceesEvents`)
"""
if self.__update_loop is not None:
self.__update_loop.close()
self.__update_loop = None
self.progressBarFinished(processEvents=None)
self.__update_loop = loop
if loop is not None:
self.progressBarInit(processEvents=None)
self.setStatusMessage("Running")
self.runbutton.setText("Stop")
self.__state = OWMDS.Running
QtGui.QApplication.postEvent(self, QEvent(QEvent.User))
else:
self.setStatusMessage("")
self.runbutton.setText("Start")
self.__state = OWMDS.Finished
def __next_step(self):
if self.__update_loop is None:
return
loop = self.__update_loop
try:
embedding, stress, progress = next(self.__update_loop)
assert self.__update_loop is loop
except StopIteration:
self.__set_update_loop(None)
self.unconditional_commit()
else:
self.progressBarSet(100.0 * progress, processEvents=None)
self.embedding = embedding
self._update_plot()
# schedule next update
QtGui.QApplication.postEvent(self, QEvent(QEvent.User),
Qt.LowEventPriority)
def customEvent(self, event):
if event.type() == QEvent.User and self.__update_loop is not None:
if not self.__in_next_step:
self.__in_next_step = True
try:
self.__next_step()
finally:
self.__in_next_step = False
else:
warnings.warn(
"Re-entry in update loop detected. "
"A rogue `proccessEvents` is on the loose.",
RuntimeWarning)
# re-schedule the update iteration.
QtGui.QApplication.postEvent(self, QEvent(QEvent.User))
return super().customEvent(event)
def __invalidate_embedding(self):
state = self.__state
if self.__update_loop is not None:
self.__set_update_loop(None)
X = self._effective_matrix.X
if self.initialization == OWMDS.PCA:
self.embedding = torgerson(X)
else:
self.embedding = numpy.random.rand(len(X), 2)
self._update_plot()
# restart the optimization if it was interrupted.
if state == OWMDS.Running:
self.__start()
def __invalidate_refresh(self):
state = self.__state
if self.__update_loop is not None:
self.__set_update_loop(None)
# restart the optimization if it was interrupted.
# TODO: decrease the max iteration count by the already
# completed iterations count.
if state == OWMDS.Running:
self.__start()
def handleNewSignals(self):
if self._invalidated:
self._invalidated = False
self._initialize()
self.start()
self._update_plot()
self.unconditional_commit()
def _invalidate_output(self):
self.commit()
def _on_color_index_changed(self):
self._pen_data = None
self._update_plot()
def _on_shape_index_changed(self):
self._shape_data = None
self._update_plot()
def _on_size_index_changed(self):
self._size_data = None
self._update_plot()
def _on_label_index_changed(self):
self._label_data = None
self._update_plot()
def _update_plot(self):
self.plot.clear()
self._scatter_item = None
self._selection_item = None
if self.embedding is not None:
self._setup_plot()
def _setup_plot(self):
have_data = self.data is not None
have_matrix_transposed = self.matrix is not None and not self.matrix.axis
def column(data, variable):
a, _ = data.get_column_view(variable)
return a.ravel()
def attributes(matrix):
return matrix.row_items.domain.attributes
def scale(a):
dmin, dmax = numpy.nanmin(a), numpy.nanmax(a)
if dmax - dmin > 0:
return (a - dmin) / (dmax - dmin)
else:
return numpy.zeros_like(a)
if self._pen_data is None:
if self._selection_mask is not None:
pointflags = numpy.where(self._selection_mask,
mdsplotutils.Selected,
mdsplotutils.NoFlags)
else:
pointflags = None
if have_data and self.color_index > 0:
color_var = self.colorvar_model[self.color_index]
if color_var.is_discrete:
palette = colorpalette.ColorPaletteGenerator(
len(color_var.values))
else:
palette = None
color_data = mdsplotutils.color_data(
self.data, color_var, plotstyle=mdsplotutils.plotstyle)
color_data = numpy.hstack((color_data,
numpy.full((len(color_data), 1),
self.symbol_opacity)))
pen_data = mdsplotutils.pen_data(color_data, pointflags)
elif have_matrix_transposed and self.colorvar_model[
self.color_index] == 'Attribute names':
attr = attributes(self.matrix)
palette = colorpalette.ColorPaletteGenerator(len(attr))
color_data = [palette.getRGB(i) for i in range(len(attr))]
color_data = numpy.hstack(
color_data,
numpy.full((len(color_data), 1), self.symbol_opacity))
pen_data = mdsplotutils.pen_data(color_data, pointflags)
else:
pen_data = make_pen(QtGui.QColor(Qt.darkGray), cosmetic=True)
pen_data = numpy.full(len(self.data), pen_data, dtype=object)
self._pen_data = pen_data
if self._shape_data is None:
if have_data and self.shape_index > 0:
Symbols = ScatterPlotItem.Symbols
symbols = numpy.array(list(Symbols.keys()))
shape_var = self.shapevar_model[self.shape_index]
data = column(self.data, shape_var)
data = data % (len(Symbols) - 1)
data[numpy.isnan(data)] = len(Symbols) - 1
shape_data = symbols[data.astype(int)]
elif have_matrix_transposed and self.shapevar_model[
self.shape_index] == 'Attribute names':
Symbols = ScatterPlotItem.Symbols
symbols = numpy.array(list(Symbols.keys()))
attr = [
i % (len(Symbols) - 1)
for i, _ in enumerate(attributes(self.matrix))
]
shape_data = symbols[attr]
else:
shape_data = "o"
self._shape_data = shape_data
if self._size_data is None:
MinPointSize = 3
point_size = self.symbol_size + MinPointSize
if have_data and self.size_index == 1:
# size by stress
size_data = stress(self.embedding, self._effective_matrix.X)
size_data = scale(size_data)
size_data = MinPointSize + size_data * point_size
elif have_data and self.size_index > 0:
size_var = self.sizevar_model[self.size_index]
size_data = column(self.data, size_var)
size_data = scale(size_data)
size_data = MinPointSize + size_data * point_size
else:
size_data = point_size
if self._label_data is None:
if have_data and self.label_index > 0:
label_var = self.labelvar_model[self.label_index]
label_data = column(self.data, label_var)
label_data = [label_var.repr_val(val) for val in label_data]
label_items = [
pg.TextItem(text, anchor=(0.5, 0)) for text in label_data
]
elif have_matrix_transposed and self.labelvar_model[
self.label_index] == 'Attribute names':
attr = attributes(self.matrix)
label_items = [
pg.TextItem(str(text), anchor=(0.5, 0)) for text in attr
]
else:
label_items = None
self._label_data = label_items
self._scatter_item = item = ScatterPlotItem(
x=self.embedding[:, 0],
y=self.embedding[:, 1],
pen=self._pen_data,
symbol=self._shape_data,
brush=QtGui.QBrush(Qt.transparent),
size=size_data,
data=numpy.arange(len(self.data)),
antialias=True)
self.plot.addItem(item)
if self._label_data is not None:
for (x, y), text_item in zip(self.embedding, self._label_data):
self.plot.addItem(text_item)
text_item.setPos(x, y)
def commit(self):
if self.embedding is not None:
output = embedding = Orange.data.Table.from_numpy(
Orange.data.Domain([
Orange.data.ContinuousVariable("X"),
Orange.data.ContinuousVariable("Y")
]), self.embedding)
else:
output = embedding = None
if self.embedding is not None and self.data is not None:
domain = self.data.domain
attrs = domain.attributes
class_vars = domain.class_vars
metas = domain.metas
if self.output_embedding_role == OWMDS.AttrRole:
attrs = attrs + embedding.domain.attributes
elif self.output_embedding_role == OWMDS.MetaRole:
metas = metas + embedding.domain.attributes
domain = Orange.data.Domain(attrs, class_vars, metas)
output = Orange.data.Table.from_table(domain, self.data)
if self.output_embedding_role == OWMDS.AttrRole:
output.X[:, -2:] = embedding.X
elif self.output_embedding_role == OWMDS.MetaRole:
output.metas[:, -2:] = embedding.X
self.send("Data", output)
if output is not None and self._selection_mask is not None and \
numpy.any(self._selection_mask):
subset = output[self._selection_mask]
else:
subset = None
self.send("Data Subset", subset)
def onDeleteWidget(self):
super().onDeleteWidget()
self.plot.clear()
self._selection_item = self._scatter_item = None
self._clear()
def __selection_end(self, path):
self.select(path)
self._pen_data = None
self._update_plot()
self._invalidate_output()
def select(self, region):
item = self._scatter_item
if item is None:
return
indices = numpy.array([
spot.data()
for spot in item.points() if region.contains(spot.pos())
],
dtype=int)
if not QtGui.QApplication.keyboardModifiers() & Qt.ControlModifier:
self._selection_mask = None
self.select_indices(indices)
def select_indices(self, indices):
if self.data is None:
return
if self._selection_mask is None:
self._selection_mask = numpy.zeros(len(self.data), dtype=bool)
self._selection_mask[indices] = True
def __init__(self, parent=None):
super().__init__(parent)
self.matrix = None
self.data = None
self.matrix_data = None
self.signal_data = None
self._pen_data = None
self._shape_data = None
self._size_data = None
self._label_data = None
self._scatter_item = None
self._selection_item = None
self._selection_mask = None
self._invalidated = False
self._effective_matrix = None
self.__update_loop = None
self.__state = OWMDS.Waiting
self.__in_next_step = False
box = gui.widgetBox(self.controlArea, "MDS Optimization")
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
)
form.addRow("Max iterations:",
gui.spin(box, self, "max_iter", 10, 10**4, step=1))
form.addRow(
"Initialization",
gui.comboBox(box,
self,
"initialization",
items=["PCA (Torgerson)", "Random"],
callback=self.__invalidate_embedding))
box.layout().addLayout(form)
form.addRow(
"Refresh",
gui.comboBox(box,
self,
"refresh_rate",
items=[t for t, _ in OWMDS.RefreshRate],
callback=self.__invalidate_refresh))
self.runbutton = gui.button(box,
self,
"Run",
callback=self._toggle_run)
box = gui.widgetBox(self.controlArea, "Graph")
self.colorvar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box,
self,
"color_index",
box="Color",
callback=self._on_color_index_changed)
cb.setModel(self.colorvar_model)
cb.box.setFlat(True)
self.shapevar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box,
self,
"shape_index",
box="Shape",
callback=self._on_shape_index_changed)
cb.setModel(self.shapevar_model)
cb.box.setFlat(True)
self.sizevar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box,
self,
"size_index",
"Size",
callback=self._on_size_index_changed)
cb.setModel(self.sizevar_model)
cb.box.setFlat(True)
self.labelvar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box,
self,
"label_index",
"Label",
callback=self._on_label_index_changed)
cb.setModel(self.labelvar_model)
cb.box.setFlat(True)
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
)
form.addRow(
"Symbol size",
gui.hSlider(box,
self,
"symbol_size",
minValue=1,
maxValue=20,
callback=self._on_size_index_changed,
createLabel=False))
form.addRow(
"Symbol opacity",
gui.hSlider(box,
self,
"symbol_opacity",
minValue=100,
maxValue=255,
step=100,
callback=self._on_color_index_changed,
createLabel=False))
box.layout().addLayout(form)
box = QtGui.QGroupBox("Zoom/Select", )
box.setLayout(QtGui.QHBoxLayout())
group = QtGui.QActionGroup(self, exclusive=True)
def icon(name):
path = "icons/Dlg_{}.png".format(name)
path = pkg_resources.resource_filename(widget.__name__, path)
return QtGui.QIcon(path)
action_select = QtGui.QAction(
"Select",
self,
checkable=True,
checked=True,
icon=icon("arrow"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_1))
action_zoom = QtGui.QAction(
"Zoom",
self,
checkable=True,
checked=False,
icon=icon("zoom"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_2))
action_pan = QtGui.QAction(
"Pan",
self,
checkable=True,
checked=False,
icon=icon("pan_hand"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_3))
action_reset_zoom = QtGui.QAction(
"Zoom to fit",
self,
icon=icon("zoom_reset"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_0))
action_reset_zoom.triggered.connect(lambda: self.plot.autoRange())
group.addAction(action_select)
group.addAction(action_zoom)
group.addAction(action_pan)
self.addActions(group.actions() + [action_reset_zoom])
action_select.setChecked(True)
def button(action):
b = QtGui.QToolButton()
b.setToolButtonStyle(Qt.ToolButtonIconOnly)
b.setDefaultAction(action)
return b
box.layout().addWidget(button(action_select))
box.layout().addWidget(button(action_zoom))
box.layout().addWidget(button(action_pan))
box.layout().addSpacing(4)
box.layout().addWidget(button(action_reset_zoom))
box.layout().addStretch()
self.controlArea.layout().addWidget(box)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, "Output")
cb = gui.comboBox(box,
self,
"output_embedding_role",
box="Append coordinates",
items=["Do not append", "As attributes", "As metas"],
callback=self._invalidate_output)
cb.box.setFlat(True)
gui.auto_commit(box,
self,
"autocommit",
"Send data",
checkbox_label="Send after any change",
box=None)
self.plot = pg.PlotWidget(background="w", enableMenu=False)
self.mainArea.layout().addWidget(self.plot)
self.selection_tool = PlotSelectionTool(
parent=self, selectionMode=PlotSelectionTool.Lasso)
self.zoom_tool = PlotZoomTool(parent=self)
self.pan_tool = PlotPanTool(parent=self)
self.pinch_tool = PlotPinchZoomTool(parent=self)
self.pinch_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.selectionFinished.connect(self.__selection_end)
self.current_tool = self.selection_tool
def activate_tool(action):
self.current_tool.setViewBox(None)
if action is action_select:
active, cur = self.selection_tool, Qt.ArrowCursor
elif action is action_zoom:
active, cur = self.zoom_tool, Qt.ArrowCursor
elif action is action_pan:
active, cur = self.pan_tool, Qt.OpenHandCursor
self.current_tool = active
self.current_tool.setViewBox(self.plot.getViewBox())
self.plot.getViewBox().setCursor(QtGui.QCursor(cur))
group.triggered[QtGui.QAction].connect(activate_tool)
class OWMDS(widget.OWWidget):
name = "MDS"
description = "Two-dimensional data projection by multidimensional " \
"scaling constructed from a distance matrix."
icon = "icons/MDS.svg"
inputs = [("Data", Orange.data.Table, "set_data"),
("Distances", Orange.misc.DistMatrix, "set_disimilarity")]
outputs = [("Data", Orange.data.Table, widget.Default),
("Data Subset", Orange.data.Table)]
#: Initialization type
PCA, Random = 0, 1
#: Refresh rate
RefreshRate = [
("Every iteration", 1),
("Every 5 steps", 5),
("Every 10 steps", 10),
("Every 25 steps", 25),
("Every 50 steps", 50),
("None", -1)
]
#: Runtime state
Running, Finished, Waiting = 1, 2, 3
settingsHandler = settings.DomainContextHandler()
max_iter = settings.Setting(300)
initialization = settings.Setting(PCA)
refresh_rate = settings.Setting(3)
# output embedding role.
NoRole, AttrRole, MetaRole = 0, 1, 2
output_embedding_role = settings.Setting(1)
autocommit = settings.Setting(True)
color_index = settings.ContextSetting(0, not_attribute=True)
shape_index = settings.ContextSetting(0, not_attribute=True)
size_index = settings.ContextSetting(0, not_attribute=True)
label_index = settings.ContextSetting(0, not_attribute=True)
symbol_size = settings.Setting(8)
symbol_opacity = settings.Setting(230)
legend_anchor = settings.Setting(((1, 0), (1, 0)))
def __init__(self, parent=None):
super().__init__(parent)
self.matrix = None
self.data = None
self.matrix_data = None
self.signal_data = None
self._pen_data = None
self._shape_data = None
self._size_data = None
self._label_data = None
self._scatter_item = None
self._legend_item = None
self._selection_mask = None
self._invalidated = False
self._effective_matrix = None
self.__update_loop = None
self.__state = OWMDS.Waiting
self.__in_next_step = False
box = gui.widgetBox(self.controlArea, "MDS Optimization")
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
)
form.addRow("Max iterations:",
gui.spin(box, self, "max_iter", 10, 10 ** 4, step=1))
form.addRow("Initialization",
gui.comboBox(box, self, "initialization",
items=["PCA (Torgerson)", "Random"],
callback=self.__invalidate_embedding))
box.layout().addLayout(form)
form.addRow("Refresh",
gui.comboBox(
box, self, "refresh_rate",
items=[t for t, _ in OWMDS.RefreshRate],
callback=self.__invalidate_refresh))
self.runbutton = gui.button(
box, self, "Run", callback=self._toggle_run)
box = gui.widgetBox(self.controlArea, "Graph")
self.colorvar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box, self, "color_index", box="Color",
callback=self._on_color_index_changed)
cb.setModel(self.colorvar_model)
cb.box.setFlat(True)
self.shapevar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box, self, "shape_index", box="Shape",
callback=self._on_shape_index_changed)
cb.setModel(self.shapevar_model)
cb.box.setFlat(True)
self.sizevar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box, self, "size_index", "Size",
callback=self._on_size_index_changed)
cb.setModel(self.sizevar_model)
cb.box.setFlat(True)
self.labelvar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box, self, "label_index", "Label",
callback=self._on_label_index_changed)
cb.setModel(self.labelvar_model)
cb.box.setFlat(True)
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
)
form.addRow("Symbol size",
gui.hSlider(box, self, "symbol_size",
minValue=1, maxValue=20,
callback=self._on_size_index_changed,
createLabel=False))
form.addRow("Symbol opacity",
gui.hSlider(box, self, "symbol_opacity",
minValue=100, maxValue=255, step=100,
callback=self._on_color_index_changed,
createLabel=False))
box.layout().addLayout(form)
box = QtGui.QGroupBox("Zoom/Select", )
box.setLayout(QtGui.QHBoxLayout())
group = QtGui.QActionGroup(self, exclusive=True)
def icon(name):
path = "icons/Dlg_{}.png".format(name)
path = pkg_resources.resource_filename(widget.__name__, path)
return QtGui.QIcon(path)
action_select = QtGui.QAction(
"Select", self, checkable=True, checked=True, icon=icon("arrow"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_1))
action_zoom = QtGui.QAction(
"Zoom", self, checkable=True, checked=False, icon=icon("zoom"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_2))
action_pan = QtGui.QAction(
"Pan", self, checkable=True, checked=False, icon=icon("pan_hand"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_3))
action_reset_zoom = QtGui.QAction(
"Zoom to fit", self, icon=icon("zoom_reset"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_0))
action_reset_zoom.triggered.connect(
lambda: self.plot.autoRange())
group.addAction(action_select)
group.addAction(action_zoom)
group.addAction(action_pan)
self.addActions(group.actions() + [action_reset_zoom])
action_select.setChecked(True)
def button(action):
b = QtGui.QToolButton()
b.setToolButtonStyle(Qt.ToolButtonIconOnly)
b.setDefaultAction(action)
return b
box.layout().addWidget(button(action_select))
box.layout().addWidget(button(action_zoom))
box.layout().addWidget(button(action_pan))
box.layout().addSpacing(4)
box.layout().addWidget(button(action_reset_zoom))
box.layout().addStretch()
self.controlArea.layout().addWidget(box)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, "Output")
cb = gui.comboBox(box, self, "output_embedding_role",
box="Append coordinates",
items=["Do not append", "As attributes", "As metas"],
callback=self._invalidate_output)
cb.box.setFlat(True)
gui.auto_commit(box, self, "autocommit", "Send data",
checkbox_label="Send after any change",
box=None)
self.plot = pg.PlotWidget(background="w", enableMenu=False)
self.mainArea.layout().addWidget(self.plot)
self.selection_tool = PlotSelectionTool(
parent=self, selectionMode=PlotSelectionTool.Lasso)
self.zoom_tool = PlotZoomTool(parent=self)
self.pan_tool = PlotPanTool(parent=self)
self.pinch_tool = PlotPinchZoomTool(parent=self)
self.pinch_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.selectionFinished.connect(self.__selection_end)
self.current_tool = self.selection_tool
def activate_tool(action):
self.current_tool.setViewBox(None)
if action is action_select:
active, cur = self.selection_tool, Qt.ArrowCursor
elif action is action_zoom:
active, cur = self.zoom_tool, Qt.ArrowCursor
elif action is action_pan:
active, cur = self.pan_tool, Qt.OpenHandCursor
self.current_tool = active
self.current_tool.setViewBox(self.plot.getViewBox())
self.plot.getViewBox().setCursor(QtGui.QCursor(cur))
group.triggered[QtGui.QAction].connect(activate_tool)
def set_data(self, data):
self.signal_data = data
if self.matrix and data is not None and len(self.matrix.X) == len(data):
self.closeContext()
self.data = data
self.update_controls()
self.openContext(data)
else:
self._invalidated = True
self._selection_mask = None
def set_disimilarity(self, matrix):
self.matrix = matrix
if matrix and matrix.row_items:
self.matrix_data = matrix.row_items
if matrix is None:
self.matrix_data = None
self._invalidated = True
self._selection_mask = None
def _clear(self):
self._pen_data = None
self._shape_data = None
self._size_data = None
self._label_data = None
self.colorvar_model[:] = ["Same color"]
self.shapevar_model[:] = ["Same shape"]
self.sizevar_model[:] = ["Same size"]
self.labelvar_model[:] = ["No labels"]
self.color_index = 0
self.shape_index = 0
self.size_index = 0
self.label_index = 0
self.__set_update_loop(None)
self.__state = OWMDS.Waiting
def _clear_plot(self):
self.plot.clear()
self._scatter_item = None
if self._legend_item is not None:
anchor = legend_anchor_pos(self._legend_item)
if anchor is not None:
self.legend_anchor = anchor
if self._legend_item.scene() is not None:
self._legend_item.scene().removeItem(self._legend_item)
self._legend_item = None
def update_controls(self):
if getattr(self.matrix, 'axis', 1) == 0:
# Column-wise distances
attr = "Attribute names"
self.labelvar_model[:] = ["No labels", attr]
self.shapevar_model[:] = ["Same shape", attr]
self.colorvar_model[:] = ["Same color", attr]
self.color_index = list(self.colorvar_model).index(attr)
self.shape_index = list(self.shapevar_model).index(attr)
else:
# initialize the graph state from data
domain = self.data.domain
all_vars = list(domain.variables + domain.metas)
cd_vars = [var for var in all_vars if var.is_primitive()]
disc_vars = [var for var in all_vars if var.is_discrete]
cont_vars = [var for var in all_vars if var.is_continuous]
str_vars = [var for var in all_vars
if var.is_discrete or var.is_string]
self.colorvar_model[:] = chain(["Same color"],
[self.colorvar_model.Separator],
cd_vars)
self.shapevar_model[:] = chain(["Same shape"],
[self.shapevar_model.Separator],
disc_vars)
self.sizevar_model[:] = chain(["Same size", "Stress"],
[self.sizevar_model.Separator],
cont_vars)
self.labelvar_model[:] = chain(["No labels"],
[self.labelvar_model.Separator],
str_vars)
if domain.class_var is not None:
self.color_index = list(self.colorvar_model).index(domain.class_var)
def _initialize(self):
# clear everything
self.closeContext()
self._clear()
self.data = None
self._effective_matrix = None
self.embedding = None
# if no data nor matrix is present reset plot
if self.signal_data is None and self.matrix is None:
self._update_plot()
return
if self.signal_data and self.matrix_data and len(self.signal_data) != len(self.matrix_data):
self.error(1, "Data and distances dimensions do not match.")
self._update_plot()
return
self.error(1)
if self.signal_data:
self.data = self.signal_data
elif self.matrix_data:
self.data = self.matrix_data
if self.matrix:
self._effective_matrix = self.matrix
if self.matrix.axis == 0:
self.data = None
else:
self._effective_matrix = Orange.distance.Euclidean(self.data)
self.update_controls()
self.openContext(self.data)
def _toggle_run(self):
if self.__state == OWMDS.Running:
self.stop()
self._invalidate_output()
else:
self.start()
def start(self):
if self.__state == OWMDS.Running:
return
elif self.__state == OWMDS.Finished:
# Resume/continue from a previous run
self.__start()
elif self.__state == OWMDS.Waiting and \
self._effective_matrix is not None:
self.__start()
def stop(self):
if self.__state == OWMDS.Running:
self.__set_update_loop(None)
def __start(self):
X = self._effective_matrix.X
if self.embedding is not None:
init = self.embedding
elif self.initialization == OWMDS.PCA:
init = torgerson(X, n_components=2)
else:
init = None
# number of iterations per single GUI update step
_, step_size = OWMDS.RefreshRate[self.refresh_rate]
if step_size == -1:
step_size = self.max_iter
def update_loop(X, max_iter, step, init):
"""
return an iterator over successive improved MDS point embeddings.
"""
# NOTE: this code MUST NOT call into QApplication.processEvents
done = False
iterations_done = 0
oldstress = numpy.finfo(numpy.float).max
while not done:
step_iter = min(max_iter - iterations_done, step)
mds = Orange.projection.MDS(
dissimilarity="precomputed", n_components=2,
n_init=1, max_iter=step_iter)
mdsfit = mds.fit(X, init=init)
iterations_done += step_iter
embedding, stress = mdsfit.embedding_, mdsfit.stress_
stress /= numpy.sqrt(numpy.sum(embedding ** 2, axis=1)).sum()
if iterations_done >= max_iter:
done = True
elif (oldstress - stress) < mds.params["eps"]:
done = True
init = embedding
oldstress = stress
yield embedding, mdsfit.stress_, iterations_done / max_iter
self.__set_update_loop(update_loop(X, self.max_iter, step_size, init))
self.progressBarInit(processEvents=None)
def __set_update_loop(self, loop):
"""
Set the update `loop` coroutine.
The `loop` is a generator yielding `(embedding, stress, progress)`
tuples where `embedding` is a `(N, 2) ndarray` of current updated
MDS points, `stress` is the current stress and `progress` a float
ratio (0 <= progress <= 1)
If an existing update loop is already in palace it is interrupted
(closed).
.. note::
The `loop` must not explicitly yield control flow to the event
loop (i.e. call `QApplication.proceesEvents`)
"""
if self.__update_loop is not None:
self.__update_loop.close()
self.__update_loop = None
self.progressBarFinished(processEvents=None)
self.__update_loop = loop
if loop is not None:
self.progressBarInit(processEvents=None)
self.setStatusMessage("Running")
self.runbutton.setText("Stop")
self.__state = OWMDS.Running
QtGui.QApplication.postEvent(self, QEvent(QEvent.User))
else:
self.setStatusMessage("")
self.runbutton.setText("Start")
self.__state = OWMDS.Finished
def __next_step(self):
if self.__update_loop is None:
return
loop = self.__update_loop
try:
embedding, stress, progress = next(self.__update_loop)
assert self.__update_loop is loop
except StopIteration:
self.__set_update_loop(None)
self.unconditional_commit()
else:
self.progressBarSet(100.0 * progress, processEvents=None)
self.embedding = embedding
self._update_plot()
# schedule next update
QtGui.QApplication.postEvent(
self, QEvent(QEvent.User), Qt.LowEventPriority)
def customEvent(self, event):
if event.type() == QEvent.User and self.__update_loop is not None:
if not self.__in_next_step:
self.__in_next_step = True
try:
self.__next_step()
finally:
self.__in_next_step = False
else:
warnings.warn(
"Re-entry in update loop detected. "
"A rogue `proccessEvents` is on the loose.",
RuntimeWarning)
# re-schedule the update iteration.
QtGui.QApplication.postEvent(self, QEvent(QEvent.User))
return super().customEvent(event)
def __invalidate_embedding(self):
state = self.__state
if self.__update_loop is not None:
self.__set_update_loop(None)
X = self._effective_matrix.X
if self.initialization == OWMDS.PCA:
self.embedding = torgerson(X)
else:
self.embedding = numpy.random.rand(len(X), 2)
self._update_plot()
# restart the optimization if it was interrupted.
if state == OWMDS.Running:
self.__start()
def __invalidate_refresh(self):
state = self.__state
if self.__update_loop is not None:
self.__set_update_loop(None)
# restart the optimization if it was interrupted.
# TODO: decrease the max iteration count by the already
# completed iterations count.
if state == OWMDS.Running:
self.__start()
def handleNewSignals(self):
if self._invalidated:
self._invalidated = False
self._initialize()
self.start()
self._update_plot()
self.unconditional_commit()
def _invalidate_output(self):
self.commit()
def _on_color_index_changed(self):
self._pen_data = None
self._update_plot()
def _on_shape_index_changed(self):
self._shape_data = None
self._update_plot()
def _on_size_index_changed(self):
self._size_data = None
self._update_plot()
def _on_label_index_changed(self):
self._label_data = None
self._update_plot()
def _update_plot(self):
self._clear_plot()
if self.embedding is not None:
self._setup_plot()
def _setup_plot(self):
have_data = self.data is not None
have_matrix_transposed = self.matrix is not None and not self.matrix.axis
def column(data, variable):
a, _ = data.get_column_view(variable)
return a.ravel()
def attributes(matrix):
return matrix.row_items.domain.attributes
def scale(a):
dmin, dmax = numpy.nanmin(a), numpy.nanmax(a)
if dmax - dmin > 0:
return (a - dmin) / (dmax - dmin)
else:
return numpy.zeros_like(a)
if self._pen_data is None:
if self._selection_mask is not None:
pointflags = numpy.where(
self._selection_mask,
mdsplotutils.Selected, mdsplotutils.NoFlags)
else:
pointflags = None
if have_data and self.color_index > 0:
color_var = self.colorvar_model[self.color_index]
if color_var.is_discrete:
palette = colorpalette.ColorPaletteGenerator(
len(color_var.values)
)
else:
palette = None
color_data = mdsplotutils.color_data(
self.data, color_var, plotstyle=mdsplotutils.plotstyle)
color_data = numpy.hstack(
(color_data,
numpy.full((len(color_data), 1), self.symbol_opacity))
)
pen_data = mdsplotutils.pen_data(color_data, pointflags)
elif have_matrix_transposed and self.colorvar_model[self.color_index] == 'Attribute names':
attr = attributes(self.matrix)
palette = colorpalette.ColorPaletteGenerator(len(attr))
color_data = [palette.getRGB(i) for i in range(len(attr))]
color_data = numpy.hstack(
color_data,
numpy.full((len(color_data), 1), self.symbol_opacity)
)
pen_data = mdsplotutils.pen_data(color_data, pointflags)
else:
pen_data = make_pen(QtGui.QColor(Qt.darkGray), cosmetic=True)
pen_data = numpy.full(len(self.data), pen_data, dtype=object)
self._pen_data = pen_data
if self._shape_data is None:
if have_data and self.shape_index > 0:
Symbols = ScatterPlotItem.Symbols
symbols = numpy.array(list(Symbols.keys()))
shape_var = self.shapevar_model[self.shape_index]
data = column(self.data, shape_var)
data = data % (len(Symbols) - 1)
data[numpy.isnan(data)] = len(Symbols) - 1
shape_data = symbols[data.astype(int)]
elif have_matrix_transposed and self.shapevar_model[self.shape_index] == 'Attribute names':
Symbols = ScatterPlotItem.Symbols
symbols = numpy.array(list(Symbols.keys()))
attr = [i % (len(Symbols) - 1) for i, _ in enumerate(attributes(self.matrix))]
shape_data = symbols[attr]
else:
shape_data = "o"
self._shape_data = shape_data
if self._size_data is None:
MinPointSize = 3
point_size = self.symbol_size + MinPointSize
if have_data and self.size_index == 1:
# size by stress
size_data = stress(self.embedding, self._effective_matrix.X)
size_data = scale(size_data)
size_data = MinPointSize + size_data * point_size
elif have_data and self.size_index > 0:
size_var = self.sizevar_model[self.size_index]
size_data = column(self.data, size_var)
size_data = scale(size_data)
size_data = MinPointSize + size_data * point_size
else:
size_data = point_size
if self._label_data is None:
if have_data and self.label_index > 0:
label_var = self.labelvar_model[self.label_index]
label_data = column(self.data, label_var)
label_data = [label_var.repr_val(val) for val in label_data]
label_items = [pg.TextItem(text, anchor=(0.5, 0))
for text in label_data]
elif have_matrix_transposed and self.labelvar_model[self.label_index] == 'Attribute names':
attr = attributes(self.matrix)
label_items = [pg.TextItem(str(text), anchor=(0.5, 0))
for text in attr]
else:
label_items = None
self._label_data = label_items
self._scatter_item = item = ScatterPlotItem(
x=self.embedding[:, 0], y=self.embedding[:, 1],
pen=self._pen_data, symbol=self._shape_data,
brush=QtGui.QBrush(Qt.transparent),
size=size_data, data=numpy.arange(len(self.data)),
antialias=True
)
self.plot.addItem(item)
if self._label_data is not None:
for (x, y), text_item in zip(self.embedding, self._label_data):
self.plot.addItem(text_item)
text_item.setPos(x, y)
self._legend_item = LegendItem()
self._legend_item.setParentItem(self.plot.getViewBox())
self._legend_item.anchor(*self.legend_anchor)
color_var = shape_var = None
if have_data and 1 <= self.color_index < len(self.colorvar_model):
color_var = self.colorvar_model[self.color_index]
assert isinstance(color_var, Orange.data.Variable)
if have_data and 1 <= self.shape_index < len(self.shapevar_model):
shape_var = self.shapevar_model[self.shape_index]
assert isinstance(shape_var, Orange.data.Variable)
if shape_var is not None or \
(color_var is not None and color_var.is_discrete):
legend_data = mdsplotutils.legend_data(
color_var, shape_var, plotstyle=mdsplotutils.plotstyle)
for color, symbol, text in legend_data:
self._legend_item.addItem(
ScatterPlotItem(pen=color, brush=color, symbol=symbol,
size=10),
text
)
else:
self._legend_item.hide()
def commit(self):
if self.embedding is not None:
output = embedding = Orange.data.Table.from_numpy(
Orange.data.Domain([Orange.data.ContinuousVariable("X"),
Orange.data.ContinuousVariable("Y")]),
self.embedding
)
else:
output = embedding = None
if self.embedding is not None and self.data is not None:
domain = self.data.domain
attrs = domain.attributes
class_vars = domain.class_vars
metas = domain.metas
if self.output_embedding_role == OWMDS.AttrRole:
attrs = attrs + embedding.domain.attributes
elif self.output_embedding_role == OWMDS.MetaRole:
metas = metas + embedding.domain.attributes
domain = Orange.data.Domain(attrs, class_vars, metas)
output = Orange.data.Table.from_table(domain, self.data)
if self.output_embedding_role == OWMDS.AttrRole:
output.X[:, -2:] = embedding.X
elif self.output_embedding_role == OWMDS.MetaRole:
output.metas[:, -2:] = embedding.X
self.send("Data", output)
if output is not None and self._selection_mask is not None and \
numpy.any(self._selection_mask):
subset = output[self._selection_mask]
else:
subset = None
self.send("Data Subset", subset)
def onDeleteWidget(self):
super().onDeleteWidget()
self._clear_plot()
self._clear()
def __selection_end(self, path):
self.select(path)
self._pen_data = None
self._update_plot()
self._invalidate_output()
def select(self, region):
item = self._scatter_item
if item is None:
return
indices = numpy.array(
[spot.data() for spot in item.points()
if region.contains(spot.pos())],
dtype=int)
if not QtGui.QApplication.keyboardModifiers() & Qt.ControlModifier:
self._selection_mask = None
self.select_indices(indices)
def select_indices(self, indices):
if self.data is None:
return
if self._selection_mask is None:
self._selection_mask = numpy.zeros(len(self.data), dtype=bool)
self._selection_mask[indices] = True
def __init__(self, parent=None):
super().__init__(parent)
self.matrix = None
self.data = None
self.matrix_data = None
self.signal_data = None
self._pen_data = None
self._shape_data = None
self._size_data = None
self._label_data = None
self._scatter_item = None
self._legend_item = None
self._selection_mask = None
self._invalidated = False
self._effective_matrix = None
self.__update_loop = None
self.__state = OWMDS.Waiting
self.__in_next_step = False
box = gui.widgetBox(self.controlArea, "MDS Optimization")
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
)
form.addRow("Max iterations:",
gui.spin(box, self, "max_iter", 10, 10 ** 4, step=1))
form.addRow("Initialization",
gui.comboBox(box, self, "initialization",
items=["PCA (Torgerson)", "Random"],
callback=self.__invalidate_embedding))
box.layout().addLayout(form)
form.addRow("Refresh",
gui.comboBox(
box, self, "refresh_rate",
items=[t for t, _ in OWMDS.RefreshRate],
callback=self.__invalidate_refresh))
self.runbutton = gui.button(
box, self, "Run", callback=self._toggle_run)
box = gui.widgetBox(self.controlArea, "Graph")
self.colorvar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box, self, "color_index", box="Color",
callback=self._on_color_index_changed)
cb.setModel(self.colorvar_model)
cb.box.setFlat(True)
self.shapevar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box, self, "shape_index", box="Shape",
callback=self._on_shape_index_changed)
cb.setModel(self.shapevar_model)
cb.box.setFlat(True)
self.sizevar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box, self, "size_index", "Size",
callback=self._on_size_index_changed)
cb.setModel(self.sizevar_model)
cb.box.setFlat(True)
self.labelvar_model = itemmodels.VariableListModel()
cb = gui.comboBox(box, self, "label_index", "Label",
callback=self._on_label_index_changed)
cb.setModel(self.labelvar_model)
cb.box.setFlat(True)
form = QtGui.QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
)
form.addRow("Symbol size",
gui.hSlider(box, self, "symbol_size",
minValue=1, maxValue=20,
callback=self._on_size_index_changed,
createLabel=False))
form.addRow("Symbol opacity",
gui.hSlider(box, self, "symbol_opacity",
minValue=100, maxValue=255, step=100,
callback=self._on_color_index_changed,
createLabel=False))
box.layout().addLayout(form)
box = QtGui.QGroupBox("Zoom/Select", )
box.setLayout(QtGui.QHBoxLayout())
group = QtGui.QActionGroup(self, exclusive=True)
def icon(name):
path = "icons/Dlg_{}.png".format(name)
path = pkg_resources.resource_filename(widget.__name__, path)
return QtGui.QIcon(path)
action_select = QtGui.QAction(
"Select", self, checkable=True, checked=True, icon=icon("arrow"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_1))
action_zoom = QtGui.QAction(
"Zoom", self, checkable=True, checked=False, icon=icon("zoom"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_2))
action_pan = QtGui.QAction(
"Pan", self, checkable=True, checked=False, icon=icon("pan_hand"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_3))
action_reset_zoom = QtGui.QAction(
"Zoom to fit", self, icon=icon("zoom_reset"),
shortcut=QtGui.QKeySequence(Qt.ControlModifier + Qt.Key_0))
action_reset_zoom.triggered.connect(
lambda: self.plot.autoRange())
group.addAction(action_select)
group.addAction(action_zoom)
group.addAction(action_pan)
self.addActions(group.actions() + [action_reset_zoom])
action_select.setChecked(True)
def button(action):
b = QtGui.QToolButton()
b.setToolButtonStyle(Qt.ToolButtonIconOnly)
b.setDefaultAction(action)
return b
box.layout().addWidget(button(action_select))
box.layout().addWidget(button(action_zoom))
box.layout().addWidget(button(action_pan))
box.layout().addSpacing(4)
box.layout().addWidget(button(action_reset_zoom))
box.layout().addStretch()
self.controlArea.layout().addWidget(box)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, "Output")
cb = gui.comboBox(box, self, "output_embedding_role",
box="Append coordinates",
items=["Do not append", "As attributes", "As metas"],
callback=self._invalidate_output)
cb.box.setFlat(True)
gui.auto_commit(box, self, "autocommit", "Send data",
checkbox_label="Send after any change",
box=None)
self.plot = pg.PlotWidget(background="w", enableMenu=False)
self.mainArea.layout().addWidget(self.plot)
self.selection_tool = PlotSelectionTool(
parent=self, selectionMode=PlotSelectionTool.Lasso)
self.zoom_tool = PlotZoomTool(parent=self)
self.pan_tool = PlotPanTool(parent=self)
self.pinch_tool = PlotPinchZoomTool(parent=self)
self.pinch_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.setViewBox(self.plot.getViewBox())
self.selection_tool.selectionFinished.connect(self.__selection_end)
self.current_tool = self.selection_tool
def activate_tool(action):
self.current_tool.setViewBox(None)
if action is action_select:
active, cur = self.selection_tool, Qt.ArrowCursor
elif action is action_zoom:
active, cur = self.zoom_tool, Qt.ArrowCursor
elif action is action_pan:
active, cur = self.pan_tool, Qt.OpenHandCursor
self.current_tool = active
self.current_tool.setViewBox(self.plot.getViewBox())
self.plot.getViewBox().setCursor(QtGui.QCursor(cur))
group.triggered[QtGui.QAction].connect(activate_tool)