def __init__(self):
super().__init__()
# The main label of the Control's GUI.
# gui.label(self.controlArea, self, "Spark Context")
self.conf = SparkConf()
all_prefedined = dict(self.conf.getAll())
# Create parameters Box.
box = gui.widgetBox(self.controlArea, "Spark Application", addSpace = True)
self.gui_parameters = OrderedDict()
main_parameters = OrderedDict()
main_parameters['spark.app.name'] = 'OrangeSpark'
main_parameters['spark.master'] = 'yarn-client'
main_parameters["spark.executor.instances"] = "8"
main_parameters["spark.executor.cores"] = "4"
main_parameters["spark.executor.memory"] = "8g"
main_parameters["spark.driver.cores"] = "4"
main_parameters["spark.driver.memory"] = "2g"
main_parameters["spark.logConf"] = "false"
main_parameters["spark.app.id"] = "dummy"
for k, v in main_parameters.items():
default_value = all_prefedined.setdefault(k, v)
self.gui_parameters[k] = GuiParam(parent_widget = box, label = k, default_value = v)
all_prefedined.pop(k)
for k, v in all_prefedined.items():
self.gui_parameters[k] = GuiParam(parent_widget = box, label = k, default_value = str(v))
action_box = gui.widgetBox(box)
# Action Button
self.create_sc_btn = gui.button(action_box, self, label = 'Submit', callback = self.create_context)
def __init__(self):
super().__init__()
self.data = None
self.input_vars = ()
self._invalidated = False
box = gui.widgetBox(self.controlArea, "Domain Features")
self.domain_model = itemmodels.VariableListModel()
self.domain_view = QListView(
selectionMode=QListView.SingleSelection
)
self.domain_view.setModel(self.domain_model)
self.domain_view.selectionModel().selectionChanged.connect(
self._on_selection_changed)
box.layout().addWidget(self.domain_view)
box = gui.widgetBox(self.controlArea, "Reset")
gui.button(box, self, "Reset selected", callback=self.reset_selected)
gui.button(box, self, "Reset all", callback=self.reset_all)
gui.auto_commit(self.controlArea, self, "autocommit", "Commit",
"Commit on change is on")
box = gui.widgetBox(self.mainArea, "Edit")
self.editor_stack = QtGui.QStackedWidget()
self.editor_stack.addWidget(DiscreteVariableEditor())
self.editor_stack.addWidget(ContinuousVariableEditor())
self.editor_stack.addWidget(VariableEditor())
box.layout().addWidget(self.editor_stack)
def __init__(self):
super().__init__()
self.data = None
self.db = None
box = gui.widgetBox(self.controlArea, "Parameters")
gui.spin(box, self, "min_samples", 1, 100, 1, callback=self._invalidate,
label="Core point neighbors")
gui.doubleSpin(box, self, "eps", 0.1, 0.9, 0.1,
callback=self._invalidate,
label="Neighborhood distance")
box = gui.widgetBox(self.controlArea, self.tr("Distance Metric"))
gui.comboBox(box, self, "metric_idx",
items=list(zip(*self.METRICS))[0],
callback=self._invalidate)
box = gui.widgetBox(self.controlArea, "Output")
gui.comboBox(box, self, "place_cluster_ids",
label="Append cluster id as ", orientation="horizontal",
callback=self.send_data, items=self.OUTPUT_METHODS)
gui.lineEdit(box, self, "output_name",
label="Name: ", orientation="horizontal",
callback=self.send_data)
gui.auto_commit(self.controlArea, self, "auto_run", "Run",
checkbox_label="Run after any change ",
orientation="horizontal")
gui.rubber(self.controlArea)
self.controlArea.setMinimumWidth(self.controlArea.sizeHint().width())
self.layout().setSizeConstraint(QtGui.QLayout.SetFixedSize)
def __init__(self):
super().__init__()
self.data = None
self.learner = None
self.preprocessors = None
self.model = None
gui.lineEdit(self.controlArea, self, 'model_name', box='Name',
tooltip='The name will identify this model in other '
'widgets')
gui.comboBox(self.controlArea, self, "attribute_score",
box='Feature selection',
items=[name for name, _ in self.scores])
box = gui.widgetBox(self.controlArea, 'Pruning')
gui.spin(box, self, "min_leaf", 1, 1000,
label="Min. instances in leaves ", checked="limit_min_leaf")
gui.spin(box, self, "min_internal", 1, 1000,
label="Stop splitting nodes with less instances than ",
checked="limit_min_internal")
gui.spin(box, self, "max_depth", 1, 1000,
label="Limit the depth to ", checked="limit_depth")
box = gui.widgetBox(self.controlArea, True, orientation="horizontal")
box.layout().addWidget(self.report_button)
gui.separator(box, 20)
self.btn_apply = gui.button(box, self, "&Apply",
callback=self.apply, disabled=0,
default=True)
self.apply()
def __init__(self):
super().__init__()
self.data = None
self.preprocessors = None
box = gui.widgetBox(self.controlArea, "Learner/Predictor Name")
gui.lineEdit(box, self, "learner_name")
box = gui.widgetBox(self.controlArea, "Regularization")
box = gui.radioButtons(
box, self, "reg_type",
btnLabels=["No regularization", "Ridge regression",
"Lasso regression"],
callback=self._reg_type_changed)
gui.separator(box)
self.alpha_box = box2 = gui.widgetBox(box, margin=0)
gui.widgetLabel(box2, "Regularization strength")
self.alpha_slider = gui.hSlider(
box2, self, "alpha_index",
minValue=0, maxValue=len(self.alphas) - 1,
callback=self._alpha_changed, createLabel=False)
box3 = gui.widgetBox(box, orientation="horizontal")
box3.layout().setAlignment(Qt.AlignCenter)
self.alpha_label = gui.widgetLabel(box3, "")
self._set_alpha_label()
gui.auto_commit(self.controlArea, self, "autosend", "Apply",
checkbox_label="Apply on every change")
self.layout().setSizeConstraint(QLayout.SetFixedSize)
self.alpha_slider.setEnabled(self.reg_type != self.OLS)
self.commit()
def add_main_layout(self):
box = gui.widgetBox(self.controlArea, "Parameters")
self.base_estimator = self.DEFAULT_BASE_ESTIMATOR
self.base_label = gui.label(
box, self, "Base estimator: " + self.base_estimator.name.title())
self.n_estimators_spin = gui.spin(
box, self, "n_estimators", 1, 100, label="Number of estimators:",
alignment=Qt.AlignRight, controlWidth=80,
callback=self.settings_changed)
self.learning_rate_spin = gui.doubleSpin(
box, self, "learning_rate", 1e-5, 1.0, 1e-5,
label="Learning rate:", decimals=5, alignment=Qt.AlignRight,
controlWidth=80, callback=self.settings_changed)
self.random_seed_spin = gui.spin(
box, self, "random_seed", 0, 2 ** 31 - 1, controlWidth=80,
label="Fixed seed for random generator:", alignment=Qt.AlignRight,
callback=self.settings_changed, checked="use_random_seed",
checkCallback=self.settings_changed)
# Algorithms
box = gui.widgetBox(self.controlArea, "Boosting method")
self.cls_algorithm_combo = gui.comboBox(
box, self, "algorithm_index", label="Classification algorithm:",
items=self.algorithms,
orientation=Qt.Horizontal, callback=self.settings_changed)
self.reg_algorithm_combo = gui.comboBox(
box, self, "loss_index", label="Regression loss function:",
items=self.losses,
orientation=Qt.Horizontal, callback=self.settings_changed)
def createExtendedContinuousPalette(self, paletteName, boxCaption,
passThroughColors=0, initialColor1=Qt.white,
initialColor2=Qt.black,
extendedPassThroughColors=((Qt.red, 1),
(Qt.black, 1),
(Qt.green, 1))):
buttBox = gui.widgetBox(self.mainArea, boxCaption)
box = gui.widgetBox(buttBox, orientation="horizontal")
self.__dict__["exCont" + paletteName + "Left"] = ColorButton(self, box, color=QColor(initialColor1))
self.__dict__["exCont" + paletteName + "View"] = PaletteView(box)
self.__dict__["exCont" + paletteName + "Right"] = ColorButton(self, box, color=QColor(initialColor2))
self.__dict__["exCont" + paletteName + "passThroughColors"] = passThroughColors
self.__dict__["exCont" + paletteName + "passThroughColorsCheckbox"] = gui.checkBox(buttBox, self,
"exCont" + paletteName + "passThroughColors",
"Use pass-through colors",
callback=self.colorSchemaChange)
box = gui.widgetBox(buttBox, "Pass-through colors", orientation="horizontal")
for i, (color, check) in enumerate(extendedPassThroughColors):
self.__dict__["exCont" + paletteName + "passThroughColor" + str(i)] = check
self.__dict__["exCont" + paletteName + "passThroughColor" + str(i) + "Checkbox"] = cb = gui.checkBox(box,
self,
"exCont" + paletteName + "passThroughColor" + str(
i),
"",
tooltip="Use color",
callback=self.colorSchemaChange)
self.__dict__["exCont" + paletteName + "color" + str(i)] = ColorButton(self, box, color=QColor(color))
if i < len(extendedPassThroughColors) - 1:
gui.rubber(box)
self.__dict__["exCont" + paletteName + "colorCount"] = len(extendedPassThroughColors)
self.exContPaletteNames.append(paletteName)
def __init__(self):
super().__init__()
gui.label(self.controlArea, self, "from pandas:")
self.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Maximum)
self.allSQLSelectWidgets.append(self) # set default settings
self.domain = None
self.recentConnections = list()
self.recentConnections.append("(none)")
self.queryFile = None
self.query = ""
self.lastQuery = None
if self.lastQuery is not None:
self.query = self.lastQuery
sources = pyodbc.dataSources()
dsns = list(sources.keys())
dsns.sort()
for dsn in dsns:
self.recentConnections.append("DSN={dsn}".format(dsn=dsn))
self.connectString = self.recentConnections[0]
self.connectBox = gui.widgetBox(self.controlArea, "Database")
self.connectLineEdit = gui.lineEdit(self.connectBox, self, "connectString", callback=None)
self.connectCombo = gui.comboBox(
self.connectBox, self, "connectString", items=self.recentConnections, valueType=str, sendSelectedValue=True
)
self.button = gui.button(self.connectBox, self, "connect", callback=self.connectDB, disabled=0)
# query
self.splitCanvas = QSplitter(QtCore.Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitCanvas)
self.textBox = gui.widgetBox(self, "HiveQL")
self.splitCanvas.addWidget(self.textBox)
self.queryTextEdit = QPlainTextEdit(self.query, self)
self.textBox.layout().addWidget(self.queryTextEdit)
self.selectBox = gui.widgetBox(self.controlArea, "Select statement")
# self.selectSubmitBox = QHGroupBox("", self.selectBox)
# self.queryTextEdit.setSizePolicy(QSizePolicy(QSizePolicy.Preferred, QSizePolicy.Preferred))
# self.queryTextEdit.setMinimumWidth(300)
# self.connect(self.queryTextEdit, SIGNAL('returnPressed()'), self.executeQuery)
gui.button(self.selectBox, self, "Open...", callback=self.openScript)
gui.button(self.selectBox, self, "Save...", callback=self.saveScript)
self.selectBox.setSizePolicy(QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.MinimumExpanding))
gui.button(self.selectBox, self, "format SQL!", callback=self.format_sql, disabled=0)
gui.button(self.selectBox, self, "execute!", callback=self.executeQuery, disabled=0)
self.domainBox = gui.widgetBox(self.controlArea, "Domain")
self.domainLabel = gui.label(self.domainBox, self, "")
# info
self.infoBox = gui.widgetBox(self.controlArea, "Info")
self.info = []
self.info.append(gui.label(self.infoBox, self, "No data loaded."))
self.info.append(gui.label(self.infoBox, self, ""))
self.resize(300, 300)
self.cnxn = None
def __init__(self):
super().__init__()
# sets self.curvePoints, self.steps equidistant points from
# 1/self.steps to 1
self.updateCurvePoints()
# [start-snippet-2]
self.scoring = [
("Classification Accuracy", Orange.evaluation.scoring.CA),
("AUC", Orange.evaluation.scoring.AUC),
("Precision", Orange.evaluation.scoring.Precision),
("Recall", Orange.evaluation.scoring.Recall)
]
# [end-snippet-2]
#: input data on which to construct the learning curve
self.data = None
#: A {input_id: Learner} mapping of current learners from input channel
self.learners = OrderedDict()
#: A {input_id: List[Results]} mapping of input id to evaluation
#: results list, one for each curve point
self.results = OrderedDict()
#: A {input_id: List[float]} mapping of input id to learning curve
#: point scores
self.curves = OrderedDict()
# GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infoa = gui.widgetLabel(box, 'No data on input.')
self.infob = gui.widgetLabel(box, 'No learners.')
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, "Evaluation Scores")
gui.comboBox(box, self, "scoringF",
items=[x[0] for x in self.scoring],
callback=self._invalidate_curves)
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, "Options")
gui.spin(box, self, 'folds', 2, 100, step=1,
label='Cross validation folds: ', keyboardTracking=False,
callback=lambda:
self._invalidate_results() if self.commitOnChange else None
)
gui.spin(box, self, 'steps', 2, 100, step=1,
label='Learning curve points: ', keyboardTracking=False,
callback=[self.updateCurvePoints,
lambda: self._invalidate_results() if self.commitOnChange else None])
gui.checkBox(box, self, 'commitOnChange', 'Apply setting on any change')
self.commitBtn = gui.button(box, self, "Apply Setting",
callback=self._invalidate_results,
disabled=True)
gui.rubber(self.controlArea)
# table widget
self.table = gui.table(self.mainArea,
selectionMode=QTableWidget.NoSelection)
def __init__(self):
super().__init__()
self.preprocessors = None
self.data = None
box = gui.widgetBox(self.controlArea, "Learner/Model Name")
gui.lineEdit(box, self, "learner_name")
box = gui.widgetBox(self.controlArea, "Neighbors")
gui.spin(box, self, "n_neighbors", 1, 100, label="Number of neighbors")
box = gui.widgetBox(box, "Metric")
box.setFlat(True)
box.layout().setContentsMargins(0, 0, 0, 0)
gui.comboBox(box, self, "metric_index",
items=["Euclidean", "Manhattan", "Maximal", "Mahalanobis"])
self.metrics = ["euclidean", "manhattan", "chebyshev", "mahalanobis"]
gui.button(self.controlArea, self, "Apply",
callback=self.apply, default=True)
self.controlArea.layout().addWidget(self.report_button)
layout = self.layout()
self.layout().setSizeConstraint(layout.SetFixedSize)
self.apply()
def __init__(self):
super().__init__()
self.data = None
self.preprocessors = None
box = gui.widgetBox(self.controlArea, self.tr("Name"))
gui.lineEdit(box, self, "learner_name")
box = gui.widgetBox(self.controlArea, box=True)
gui.comboBox(box, self, "penalty_type", label="Regularization type: ",
items=self.penalty_types,
orientation="horizontal", addSpace=4)
gui.widgetLabel(box, "Strength:")
box2 = gui.widgetBox(gui.indentedBox(box), orientation="horizontal")
gui.widgetLabel(box2, "Weak").setStyleSheet("margin-top:6px")
gui.hSlider(box2, self, "C_index",
minValue=0, maxValue=len(self.C_s) - 1,
callback=self.set_c, createLabel=False)
gui.widgetLabel(box2, "Strong").setStyleSheet("margin-top:6px")
box2 = gui.widgetBox(box, orientation="horizontal")
box2.layout().setAlignment(Qt.AlignCenter)
self.c_label = gui.widgetLabel(box2)
box = gui.widgetBox(self.controlArea, orientation="horizontal",
margin=0)
box.layout().addWidget(self.report_button)
gui.button(box, self, "&Apply", callback=self.apply, default=True)
self.set_c()
self.apply()
def __init__(self, parent=None):
widget.OWWidget.__init__(self, parent)
box = gui.widgetBox(self.controlArea, "Multinomial attributes")
gui.radioButtonsInBox(
box, self, "multinomial_treatment",
btnLabels=[x[0] for x in self.multinomial_treats],
callback=self.settings_changed)
box = gui.widgetBox(self.controlArea, "Continuous attributes")
gui.radioButtonsInBox(
box, self, "continuous_treatment",
btnLabels=[x[0] for x in self.continuous_treats],
callback=self.settings_changed)
box = gui.widgetBox(self.controlArea, "Discrete class attribute")
gui.radioButtonsInBox(
box, self, "class_treatment",
btnLabels=[t[0] for t in self.class_treats],
callback=self.settings_changed)
zbbox = gui.widgetBox(self.controlArea, "Value range")
gui.radioButtonsInBox(
zbbox, self, "zero_based",
btnLabels=self.value_ranges,
callback=self.settings_changed)
gui.auto_commit(self.controlArea, self, "autosend", "Apply")
self.data = None
self.resize(150, 300)
def __init__(self):
super().__init__()
self.data = None
grid = QGridLayout()
gui.widgetBox(self.controlArea, orientation=grid)
grid.addWidget(
gui.checkBox(
None, self, "add_type_annotations",
"Add type annotations to header",
tooltip=
"Some formats (Tab-delimited, Comma-separated) can include \n"
"additional information about variables types in header rows.",
callback=self._update_messages),
0, 0, 1, 2)
grid.setRowMinimumHeight(1, 8)
grid.addWidget(
gui.checkBox(
None, self, "auto_save", "Autosave when receiving new data",
callback=self._update_messages),
2, 0, 1, 2)
grid.setRowMinimumHeight(3, 8)
self.bt_save = gui.button(None, self, "Save", callback=self.save_file)
grid.addWidget(self.bt_save, 4, 0)
grid.addWidget(
gui.button(None, self, "Save as ...", callback=self.save_file_as),
4, 1)
self.adjustSize()
self._update_messages()
def __init__(self):
super().__init__()
self.data = None
self.removedAttrs = "-"
self.reducedAttrs = "-"
self.resortedAttrs = "-"
self.removedClasses = "-"
self.reducedClasses = "-"
self.resortedClasses = "-"
boxAt = gui.widgetBox(self.controlArea, "Features")
for not_first, (value, label) in enumerate(self.feature_options):
if not_first:
gui.separator(boxAt, 2)
gui.checkBox(boxAt, self, value, label,
callback=self.optionsChanged)
boxAt = gui.widgetBox(self.controlArea, "Classes", addSpace=True)
for not_first, (value, label) in enumerate(self.class_options):
if not_first:
gui.separator(boxAt, 2)
gui.checkBox(boxAt, self, value, label,
callback=self.optionsChanged)
box3 = gui.widgetBox(self.controlArea, 'Statistics', addSpace=True)
for label, value in self.stat_labels:
gui.label(box3, self, "{}: %({})s".format(label, value))
gui.auto_commit(self.controlArea, self, "autoSend", "Send Data",
checkbox_label="Send automatically",
orientation="horizontal")
gui.rubber(self.controlArea)
def _create_layout(self):
self._new_webview()
box = gui.widgetBox(self.controlArea, 'Info')
self.topic_info = gui.label(box, self, '%(n_topic_words)d words in a topic')
gui.label(box, self, '%(documents_info_str)s')
box = gui.widgetBox(self.controlArea, 'Cloud preferences')
gui.checkBox(box, self, 'words_color', 'Color words', callback=self.on_cloud_pref_change)
TILT_VALUES = ('no', 'slight', 'more', 'full')
gui.valueSlider(box, self, 'words_tilt', label='Words tilt:',
values=list(range(len(TILT_VALUES))),
callback=self.on_cloud_pref_change,
labelFormat=lambda x: TILT_VALUES[x])
gui.button(box, None, 'Regenerate word cloud', callback=self.on_cloud_pref_change)
box = gui.widgetBox(self.controlArea, 'Words && weights')
self.table = gui.TableWidget(box,
col_labels=['Weight', 'Word'],
multi_selection=True,
select_rows=True)
def _selection_changed(selected, deselected):
for index in deselected.indexes():
data = self.table.rowData(index.row())
self.selected_words.remove(data)
for index in selected.indexes():
data = self.table.rowData(index.row())
self.selected_words.add(data)
self.cloud_reselect()
self.table.selectionChanged = _selection_changed
def _create_layout(self):
self.mainArea.layout().addWidget(self.graphview)
info = gui.widgetBox(self.controlArea, 'Info')
gui.label(info, self, '%(n_object_types)d object types')
gui.label(info, self, '%(n_relations)d relations')
# Table view of relation details
info = gui.widgetBox(self.controlArea, 'Relations')
class TableView(gui.TableView):
def __init__(self, parent=None, **kwargs):
super().__init__(parent, **kwargs)
self._parent = parent
self.bold_font = self.BoldFontDelegate(self) # member because PyQt sometimes unrefs too early
self.setItemDelegateForColumn(2, self.bold_font)
self.setItemDelegateForColumn(4, self.bold_font)
self.horizontalHeader().setVisible(False)
def selectionChanged(self, selected, deselected):
super().selectionChanged(selected, deselected)
if not selected:
assert len(deselected) > 0
relation = None
else:
assert len(selected) == 1
data = self._parent.tablemodel[selected[0].top()][0]
relation = Relation(data)
self._parent.send(Output.RELATION, relation)
model = self.tablemodel = PyTableModel(parent=self)
table = self.table = TableView(self,
selectionMode=TableView.SingleSelection)
table.setModel(model)
info.layout().addWidget(self.table)
gui.lineEdit(self.controlArea,
self, 'pref_algo_name', 'Fuser name:',
orientation='horizontal',
callback=self.checkcommit, enterPlaceholder=True)
gui.radioButtons(self.controlArea,
self, 'pref_algorithm', [i[0] for i in DECOMPOSITION_ALGO],
box='Decomposition algorithm',
callback=self.checkcommit)
gui.radioButtons(self.controlArea,
self, 'pref_initialization', INITIALIZATION_ALGO,
box='Initialization algorithm',
callback=self.checkcommit)
slider = gui.hSlider(
self.controlArea, self, 'pref_n_iterations',
'Maximum number of iterations',
minValue=10, maxValue=500, createLabel=True,
callback=self.checkcommit)
slider.setTracking(False)
self.slider_rank = gui.hSlider(self.controlArea, self, 'pref_rank',
'Factorization rank',
minValue=1, maxValue=100, createLabel=True,
labelFormat=" %d%%",
callback=self.checkcommit)
self.slider_rank.setTracking(False)
gui.auto_commit(self.controlArea, self, "autorun", "Run",
checkbox_label="Run after any change ")
def __init__(self, parent, windowTitle="New York Times API key"):
super().__init__(parent, windowTitle=windowTitle)
self.parent = parent
self.setLayout(QVBoxLayout())
self.layout().setMargin(10)
self.mainArea = gui.widgetBox(self)
self.layout().addWidget(self.mainArea)
# Combo box.
self.api_key_combo = QComboBox(self.mainArea)
self.api_key_combo.setEditable(True)
self.api_key_combo.activated[int].connect(self.select_api_key)
self.mainArea.layout().addWidget(self.api_key_combo)
# Buttons
self.button_box = gui.widgetBox(self.mainArea, orientation="horizontal")
gui.button(self.button_box, self, "Check", self.check_api_key)
gui.button(self.button_box, self, "OK", self.accept_changes)
gui.button(self.button_box, self, "Cancel", self.reject_changes)
# Label
self.label_box = gui.widgetBox(self, orientation="horizontal")
self.api_key_check_label = gui.label(self.label_box, self, "")
if self.parent.api_key_is_valid:
self.api_key_check_label.setText("API key is valid.")
else:
self.api_key_check_label.setText("API key NOT validated!")
# Load the most recent API keys.
self.set_key_list()
def _add_controls(self):
infobox = gui.widgetBox(self.controlArea, "Info")
self.infoLabel = gui.widgetLabel(infobox, "No data on input.")
displaybox = gui.widgetBox(self.controlArea, "Display")
gui.checkBox(displaybox, self, "show_profiles", "Lines",
callback=self.__show_profiles_changed,
tooltip="Plot lines")
gui.checkBox(displaybox, self, "show_range", "Range",
callback=self.__show_range_changed,
tooltip="Plot range between 10th and 90th percentile")
gui.checkBox(displaybox, self, "show_mean", "Mean",
callback=self.__show_mean_changed,
tooltip="Plot mean curve")
gui.checkBox(displaybox, self, "show_error", "Error bars",
callback=self.__show_error_changed,
tooltip="Show standard deviation")
self.group_vars = DomainModel(
placeholder="None", separators=False, valid_types=DiscreteVariable)
self.group_view = gui.listView(
self.controlArea, self, "group_var", box="Group by",
model=self.group_vars, callback=self.__group_var_changed)
self.group_view.setEnabled(False)
self.group_view.setMinimumSize(QSize(30, 100))
self.group_view.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Ignored)
plot_gui = OWPlotGUI(self)
plot_gui.box_zoom_select(self.controlArea)
gui.rubber(self.controlArea)
gui.auto_commit(self.controlArea, self, "auto_commit",
"Send Selection", "Send Automatically")
def __init__(self, parent=None):
super().__init__(parent)
self.data = None
self.preprocessors = None
box = gui.widgetBox(self.controlArea, "Learner/Predictor Name")
gui.lineEdit(box, self, "learner_name")
box = gui.widgetBox(self.controlArea, "Options")
box = gui.radioButtons(box, self, "reg_type",
callback=self._reg_type_changed)
gui.appendRadioButton(box, "Ordinary linear regression")
gui.appendRadioButton(box, "Ridge regression")
ibox = gui.indentedBox(box)
gui.doubleSpin(ibox, self, "ridgealpha", 0.0, 1000.0, label="alpha:")
self.ridge_box = ibox
gui.appendRadioButton(box, "Lasso regression")
ibox = gui.indentedBox(box)
gui.doubleSpin(ibox, self, "lassoalpha", 0.0, 1000.0, label="alpha")
self.lasso_box = ibox
gui.button(self.controlArea, self, "Apply", callback=self.apply,
default=True)
self.layout().setSizeConstraint(QLayout.SetFixedSize)
self.ridge_box.setEnabled(self.reg_type == self.Ridge)
self.lasso_box.setEnabled(self.reg_type == self.Lasso)
self.apply()
def __init__(self):
super().__init__()
self.corpus = None
self.preprocessor = None
self.normalization = None
# Pre-processing info.
pp_info_box = gui.widgetBox(self.controlArea, "Pre-processing info")
pp_info = "Includes punctuation: {}\n" \
"Lowercase: {}\n" \
"Transformation: {}\n" \
"Stop words removed: {}\n" \
"TF-IDF performed: {}\n" \
"Normalization: {}"\
.format(False, False, None, None,
self.use_tfidf, self.normalization)
self.pp_info_label = gui.label(pp_info_box, self, pp_info)
# TF-IDF.
tfidf_box = gui.widgetBox(self.controlArea, "TF-IDF", addSpace=False)
self.tfidf_chbox = gui.checkBox(tfidf_box, self, "use_tfidf", "Use TF-IDF")
self.tfidf_chbox.stateChanged.connect(self._tfidf_changed)
ibox = gui.indentedBox(tfidf_box)
self.norm_combo = gui.comboBox(ibox, self, 'normalization_type',
items=self._normalization_options,
label="Normalization:")
self.norm_combo.activated[int].connect(self._select_normalization)
self.norm_combo.setEnabled(self.use_tfidf)
gui.button(self.controlArea, self, "&Apply", callback=self.apply, default=True)
def __init__(self):
super().__init__()
# options box
self.options_box = gui.widgetBox(self.controlArea, "Data")
opts = dict(
widget=self.options_box, master=self, orientation=Qt.Horizontal,
callback=self.restart, sendSelectedValue=True,
maximumContentsLength=15)
self.cbx = gui.comboBox(value='attr_x', label='X: ', **opts)
self.cby = gui.comboBox(value='attr_y', label='Y: ', **opts)
self.centroids_box = gui.widgetBox(self.controlArea, "Centroids")
self.centroid_numbers_spinner = gui.spin(
self.centroids_box, self, 'number_of_clusters',
minv=1, maxv=10, step=1, label='Number of centroids:',
alignment=Qt.AlignRight, callback=self.number_of_clusters_change)
self.restart_button = gui.button(
self.centroids_box, self, "Randomize Positions",
callback=self.restart)
gui.separator(self.centroids_box)
self.lines_checkbox = gui.checkBox(
self.centroids_box, self, 'lines_to_centroids',
'Show membership lines', callback=self.complete_replot)
# control box
gui.separator(self.controlArea, 20, 20)
self.step_box = gui.widgetBox(self.controlArea, "Manually step through")
self.step_button = gui.button(
self.step_box, self, self.STEP_BUTTONS[1], callback=self.step)
self.step_back_button = gui.button(
self.step_box, self, "Step Back", callback=self.step_back)
self.run_box = gui.widgetBox(self.controlArea, "Run")
self.auto_play_speed_spinner = gui.hSlider(
self.run_box, self, 'auto_play_speed', label='Speed:',
minValue=0, maxValue=1.91, step=0.1, intOnly=False,
createLabel=False)
self.auto_play_button = gui.button(
self.run_box, self, self.AUTOPLAY_BUTTONS[0],
callback=self.auto_play)
gui.rubber(self.controlArea)
# disable until data loaded
self.set_disabled_all(True)
# graph in mainArea
self.scatter = Scatterplot(
click_callback=self.graph_clicked,
drop_callback=self.centroid_dropped,
xAxis_gridLineWidth=0, yAxis_gridLineWidth=0,
tooltip_enabled=False,
debug=False)
# Just render an empty chart so it shows a nice 'No data to display'
self.scatter.chart()
self.mainArea.layout().addWidget(self.scatter)
def __init__(self):
super().__init__()
self.data = None
self.orig_domain = None
self.disc_colors = []
self.cont_colors = []
box = gui.widgetBox(self.controlArea, "Discrete variables",
orientation="horizontal")
self.disc_model = DiscColorTableModel()
disc_view = self.disc_view = DiscreteTable(self.disc_model)
disc_view.horizontalHeader().setResizeMode(QHeaderView.ResizeToContents)
self.disc_model.dataChanged.connect(self._on_data_changed)
box.layout().addWidget(disc_view)
box = gui.widgetBox(self.controlArea, "Numeric variables",
orientation="horizontal")
self.cont_model = ContColorTableModel()
cont_view = self.cont_view = ContinuousTable(self, self.cont_model)
cont_view.setColumnWidth(1, 256)
self.cont_model.dataChanged.connect(self._on_data_changed)
box.layout().addWidget(cont_view)
box = gui.auto_commit(self.controlArea, self, "auto_apply", "Send data",
orientation="horizontal",
checkbox_label="Resend data on every change")
box.layout().insertSpacing(0, 20)
box.layout().insertWidget(0, self.report_button)
def _add_kernel_box(self):
# Initialize with the widest label to measure max width
self.kernel_eq = self.kernels[-1][1]
self.kernel_box = box = gui.widgetBox(
self.controlArea, "Kernel", orientation="horizontal")
buttonbox = gui.radioButtonsInBox(
box, self, "kernel_type", btnLabels=[k[0] for k in self.kernels],
callback=self._on_kernel_changed, addSpace=20)
buttonbox.layout().setSpacing(10)
gui.rubber(buttonbox)
parambox = gui.widgetBox(box)
gui.label(parambox, self, "Kernel: %(kernel_eq)s")
common = dict(orientation="horizontal",
alignment=Qt.AlignRight, controlWidth=80)
spbox = gui.widgetBox(parambox, orientation="horizontal")
gui.rubber(spbox)
inbox = gui.widgetBox(spbox)
gamma = gui.doubleSpin(
inbox, self, "gamma", 0.0, 10.0, 0.01, label=" g: ", **common)
coef0 = gui.doubleSpin(
inbox, self, "coef0", 0.0, 10.0, 0.01, label=" c: ", **common)
degree = gui.doubleSpin(
inbox, self, "degree", 0.0, 10.0, 0.5, label=" d: ", **common)
self._kernel_params = [gamma, coef0, degree]
gui.rubber(parambox)
# This is the maximal height (all double spins are visible)
# and the maximal width (the label is initialized to the widest one)
box.layout().activate()
box.setFixedHeight(box.sizeHint().height())
box.setMinimumWidth(box.sizeHint().width())
def __init__(self, parent=None):
super().__init__(parent)
self.train_data = None
self.test_data = None
#: An Ordered dictionary with current inputs and their testing
#: results.
self.learners = OrderedDict()
sbox = gui.widgetBox(self.controlArea, "Sampling")
rbox = gui.radioButtons(
sbox, self, "resampling", callback=self._param_changed
)
gui.appendRadioButton(rbox, "Cross validation")
ibox = gui.indentedBox(rbox)
gui.spin(ibox, self, "k_folds", 2, 50, label="Number of folds:",
callback=self.kfold_changed)
gui.appendRadioButton(rbox, "Leave one out")
gui.appendRadioButton(rbox, "Random sampling")
ibox = gui.indentedBox(rbox)
gui.spin(ibox, self, "n_repeat", 2, 50, label="Repeat train/test",
callback=self.bootstrap_changed)
gui.widgetLabel(ibox, "Relative training set size:")
gui.hSlider(ibox, self, "sample_p", minValue=1, maxValue=100,
ticks=20, vertical=False, labelFormat="%d %%",
callback=self.bootstrap_changed)
gui.appendRadioButton(rbox, "Test on train data")
gui.appendRadioButton(rbox, "Test on test data")
rbox.layout().addSpacing(5)
gui.button(rbox, self, "Apply", callback=self.apply)
self.cbox = gui.widgetBox(self.controlArea, "Target class")
self.class_selection_combo = gui.comboBox(self.cbox, self, "class_selection",
items=[],
callback=self._select_class,
sendSelectedValue=True, valueType=str)
gui.rubber(self.controlArea)
self.view = QTreeView(
rootIsDecorated=False,
uniformRowHeights=True,
wordWrap=True,
editTriggers=QTreeView.NoEditTriggers
)
header = self.view.header()
header.setResizeMode(QHeaderView.ResizeToContents)
header.setDefaultAlignment(Qt.AlignCenter)
header.setStretchLastSection(False)
self.result_model = QStandardItemModel()
self.view.setModel(self.result_model)
self.view.setItemDelegate(ItemDelegate())
self._update_header()
box = gui.widgetBox(self.mainArea, "Evaluation Results")
box.layout().addWidget(self.view)
def __init__(self):
super().__init__()
# Control GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infolabel = gui.widgetLabel(
box, "No data on input\nPredictors: 0\nTask: N/A"
)
self.infolabel.setMinimumWidth(200)
box = gui.widgetBox(self.controlArea, "Options")
self.checkbox_class = gui.checkBox(box, self, "show_class",
"Show predicted class",
callback=self.flipClass)
self.checkbox_prob = gui.checkBox(box, self, "show_probabilities",
"Show predicted probabilities",
callback=self.flipProb)
QtGui.qApp.processEvents()
QtCore.QTimer.singleShot(0, self.fix_size)
#: input data
self.data = None
#: A dict mapping input ids to PredictorSlot
self.predictors = OrderedDict()
#: A class variable (prediction target)
self.class_var = None
def __init__(self, parent=None, signalManager=None, stored_settings=None):
super(OWSql, self).__init__(parent=parent,
signalManager=signalManager,
stored_settings=stored_settings)
self._connection = None
vbox = gui.widgetBox(self.controlArea, "Server", addSpace=True)
box = gui.widgetBox(vbox)
self.servertext = QtGui.QLineEdit(box)
self.servertext.setPlaceholderText('Server')
if self.host:
self.servertext.setText(self.host if not self.port else
'{}:{}'.format(self.host, self.port))
box.layout().addWidget(self.servertext)
self.databasetext = QtGui.QLineEdit(box)
self.databasetext.setPlaceholderText('Database')
if self.database:
self.databasetext.setText(self.database)
box.layout().addWidget(self.databasetext)
self.usernametext = QtGui.QLineEdit(box)
self.usernametext.setPlaceholderText('Username')
if self.username:
self.usernametext.setText(self.username)
box.layout().addWidget(self.usernametext)
self.passwordtext = QtGui.QLineEdit(box)
self.passwordtext.setPlaceholderText('Password')
self.passwordtext.setEchoMode(QtGui.QLineEdit.Password)
if self.password:
self.passwordtext.setText(self.password)
box.layout().addWidget(self.passwordtext)
tables = gui.widgetBox(box, orientation='horizontal')
self.tablecombo = QtGui.QComboBox(tables)
tables.layout().addWidget(self.tablecombo)
self.tablecombo.activated[int].connect(self.select_table)
self.connectbutton = gui.button(
tables, self, '↻', callback=self.connect)
self.connectbutton.setSizePolicy(
QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
tables.layout().addWidget(self.connectbutton)
self.custom_sql = gui.widgetBox(box, orientation='vertical')
self.custom_sql.setVisible(False)
self.sqltext = QtGui.QTextEdit(self.custom_sql)
self.sqltext.setPlainText(self.sql)
self.custom_sql.layout().addWidget(self.sqltext)
self.executebtn = gui.button(
self.custom_sql, self, 'Execute', callback=self.open_table)
box.layout().addWidget(self.custom_sql)
gui.checkBox(box, self, "guess_values",
"Auto-discover discrete variables.",
callback=self.open_table)
self.connect()
if self.table:
self.open_table()
def _setup_layout(self):
self.controlArea.setMinimumWidth(self.controlArea.sizeHint().width())
self.layout().setSizeConstraint(QLayout.SetFixedSize)
widget_box = widgetBox(self.controlArea, 'Info')
self.input_data_info = widgetLabel(widget_box, self._NO_DATA_INFO_TEXT)
self.connection_info = widgetLabel(widget_box, "")
widget_box = widgetBox(self.controlArea, 'Settings')
self.cb_image_attr = comboBox(
widget=widget_box,
master=self,
value='cb_image_attr_current_id',
label='Image attribute:',
orientation=Qt.Horizontal,
callback=self._cb_image_attr_changed
)
self.auto_commit_widget = auto_commit(
widget=self.controlArea,
master=self,
value='_auto_apply',
label='Apply',
checkbox_label='Auto Apply',
commit=self.commit
)
def __init__(self):
super().__init__()
gui.label(self.controlArea, self, "Spark DataFrame")
self.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Maximum)
self.allSQLSelectWidgets.append(self) # set default settings
self.domain = None
self.queryFile = None
self.query = ''
self.lastQuery = None
# self.loadSettings()
if self.lastQuery is not None:
self.query = self.lastQuery
# query
self.splitCanvas = QSplitter(QtCore.Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitCanvas)
self.textBox = gui.widgetBox(self, 'SparkSQL')
self.splitCanvas.addWidget(self.textBox)
self.queryTextEdit = QPlainTextEdit(self.query, self)
self.textBox.layout().addWidget(self.queryTextEdit)
self.selectBox = gui.widgetBox(self.controlArea, "Select statement")
self.selectBox.setSizePolicy(QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.MinimumExpanding))
gui.button(self.selectBox, self, 'format SQL!', callback = self.format_sql, disabled = 0)
gui.button(self.selectBox, self, 'execute!', callback = self.executeQuery, disabled = 0)
# info
self.infoBox = gui.widgetBox(self.controlArea, "Info")
self.info = []
self.info.append(gui.label(self.infoBox, self, 'No data loaded.'))
self.info.append(gui.label(self.infoBox, self, ''))
self.resize(300, 300)
def __init__(self):
super().__init__()
self.data = None
"""The LazyTable that will be send."""
# GUI: as simple as possible for now
box = gui.widgetBox(self.controlArea, "SAMP Info")
self.infoa = gui.widgetLabel(widget=box, label='SAMP status unknown.')
box_input_catalog = gui.widgetBox(box, orientation=0)
self.input_catalog_text = gui.widgetLabel(widget=box_input_catalog , label='Catalog')
self.input_catalog = gui.lineEdit(widget=box_input_catalog , master=self, value='catalog_of_interest')
#self.resize(100,50)
self.button_disconnect = gui.button(self.controlArea, self, "&Disconnect", callback=self.disconnect_samp, default=False)
self.button_connect = gui.button(self.controlArea, self, "&Connect", callback=self.connect_samp, default=False)
self.button_disconnect.setHidden(True)
#gui.button(self.controlArea, self, "&Pull Rows", callback=self.pull_rows, default=False)
gui.button(self.controlArea, self, "&Set Table", callback=self.we_have_a_new_table, default=False)
# Create a SAMP client and connect to HUB.
# Do not make the client in __init__ because this does not allow
# the client to disconnect and reconnect again.
self.samp_client = None
self.connect_samp()
def __init__(self):
super().__init__()
# The main label of the Control's GUI.
# gui.label(self.controlArea, self, "Spark Context")
# Create parameters Box.
box = gui.widgetBox(self.controlArea, "Spark SQL Table", addSpace = True)
self.gui_parameters = OrderedDict()
if self.hc:
self.databases = [i.result for i in self.hc.sql("show databases").collect()]
default_value = self.saved_gui_params.get('database', 'default')
if default_value not in self.databases:
self.databases.append(default_value)
self.database = default_value
self.refresh_databases_btn = gui.button(box, self, label = 'Refresh databases', callback = self.fill_database_list)
self.gui_parameters['database'] = GuiParam(parent_widget = box, list_values = self.databases, label = 'Database', default_value = default_value,
callback_func = self.refresh_database)
default_value = self.saved_gui_params.get('table', '')
self.gui_parameters['table'] = GuiParam(parent_widget = box, label = 'Table', default_value = default_value, list_values = [default_value])
self.refresh_database(self.gui_parameters['database'].get_value())
action_box = gui.widgetBox(box)
# Action Button
self.create_sc_btn = gui.button(action_box, self, label = 'Submit', callback = self.submit)
def __init__(self, parent=None):
super().__init__(parent)
self.matrix = None
self.items = None
self.linkmatrix = None
self.root = None
self._displayed_root = None
self.cutoff_height = 0.0
gui.comboBox(gui.widgetBox(self.controlArea, "Linkage"),
self,
"linkage",
items=LINKAGE,
callback=self._invalidate_clustering)
box = gui.widgetBox(self.controlArea, "Annotation")
self.label_cb = gui.comboBox(box,
self,
"annotation_idx",
callback=self._update_labels)
self.label_cb.setModel(itemmodels.VariableListModel())
self.label_cb.model()[:] = ["None", "Enumeration"]
box = gui.radioButtons(self.controlArea,
self,
"pruning",
box="Pruning",
callback=self._invalidate_pruning)
grid = QGridLayout()
box.layout().addLayout(grid)
grid.addWidget(gui.appendRadioButton(box, "None", addToLayout=False),
0, 0)
self.max_depth_spin = gui.spin(box,
self,
"max_depth",
minv=1,
maxv=100,
callback=self._invalidate_pruning,
keyboardTracking=False)
grid.addWidget(
gui.appendRadioButton(box, "Max depth", addToLayout=False), 1, 0)
grid.addWidget(self.max_depth_spin, 1, 1)
box = gui.radioButtons(self.controlArea,
self,
"selection_method",
box="Selection",
callback=self._selection_method_changed)
grid = QGridLayout()
box.layout().addLayout(grid)
grid.addWidget(gui.appendRadioButton(box, "Manual", addToLayout=False),
0, 0)
grid.addWidget(
gui.appendRadioButton(box, "Height ratio", addToLayout=False), 1,
0)
self.cut_ratio_spin = gui.spin(box,
self,
"cut_ratio",
0,
100,
step=1e-1,
spinType=float,
callback=self._selection_method_changed)
self.cut_ratio_spin.setSuffix("%")
grid.addWidget(self.cut_ratio_spin, 1, 1)
grid.addWidget(gui.appendRadioButton(box, "Top N", addToLayout=False),
2, 0)
self.top_n_spin = gui.spin(box,
self,
"top_n",
1,
20,
callback=self._selection_method_changed)
grid.addWidget(self.top_n_spin, 2, 1)
box.layout().addLayout(grid)
self.controlArea.layout().addStretch()
box = gui.widgetBox(self.controlArea, "Output")
gui.checkBox(box,
self,
"append_clusters",
"Append cluster IDs",
callback=self._invalidate_output)
ibox = gui.indentedBox(box)
name_edit = gui.lineEdit(ibox, self, "cluster_name")
name_edit.editingFinished.connect(self._invalidate_output)
cb = gui.comboBox(
ibox,
self,
"cluster_role",
callback=self._invalidate_output,
items=["Attribute", "Class variable", "Meta variable"])
form = QFormLayout(fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow,
labelAlignment=Qt.AlignLeft,
spacing=8)
form.addRow("Name", name_edit)
form.addRow("Place", cb)
ibox.layout().addSpacing(5)
ibox.layout().addLayout(form)
ibox.layout().addSpacing(5)
gui.auto_commit(box,
self,
"autocommit",
"Send data",
"Auto send is on",
box=False)
self.scene = QGraphicsScene()
self.view = QGraphicsView(
self.scene,
horizontalScrollBarPolicy=Qt.ScrollBarAlwaysOff,
verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn,
alignment=Qt.AlignLeft | Qt.AlignVCenter)
def axis_view(orientation):
ax = pg.AxisItem(orientation=orientation, maxTickLength=7)
scene = QGraphicsScene()
scene.addItem(ax)
view = QGraphicsView(
scene,
horizontalScrollBarPolicy=Qt.ScrollBarAlwaysOff,
verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn,
alignment=Qt.AlignLeft | Qt.AlignVCenter)
view.setFixedHeight(ax.size().height())
ax.line = SliderLine(orientation=Qt.Horizontal,
length=ax.size().height())
scene.addItem(ax.line)
return view, ax
self.top_axis_view, self.top_axis = axis_view("top")
self.mainArea.layout().setSpacing(1)
self.mainArea.layout().addWidget(self.top_axis_view)
self.mainArea.layout().addWidget(self.view)
self.bottom_axis_view, self.bottom_axis = axis_view("bottom")
self.mainArea.layout().addWidget(self.bottom_axis_view)
self._main_graphics = QGraphicsWidget()
self._main_layout = QGraphicsLinearLayout(Qt.Horizontal)
self._main_layout.setSpacing(1)
self._main_graphics.setLayout(self._main_layout)
self.scene.addItem(self._main_graphics)
self.dendrogram = DendrogramWidget()
self.dendrogram.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
self.dendrogram.selectionChanged.connect(self._invalidate_output)
self.dendrogram.selectionEdited.connect(self._selection_edited)
fm = self.fontMetrics()
self.dendrogram.setContentsMargins(5,
fm.lineSpacing() / 2, 5,
fm.lineSpacing() / 2)
self.labels = GraphicsSimpleTextList()
self.labels.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Preferred)
self.labels.setAlignment(Qt.AlignLeft)
self.labels.setMaximumWidth(200)
self.labels.layout().setSpacing(0)
self._main_layout.addItem(self.dendrogram)
self._main_layout.addItem(self.labels)
self._main_layout.setAlignment(self.dendrogram,
Qt.AlignLeft | Qt.AlignVCenter)
self._main_layout.setAlignment(self.labels,
Qt.AlignLeft | Qt.AlignVCenter)
self.view.viewport().installEventFilter(self)
self.top_axis_view.viewport().installEventFilter(self)
self.bottom_axis_view.viewport().installEventFilter(self)
self._main_graphics.installEventFilter(self)
self.cut_line = SliderLine(self.dendrogram, orientation=Qt.Horizontal)
self.cut_line.valueChanged.connect(self._dendrogram_slider_changed)
self.cut_line.hide()
self.bottom_axis.line.valueChanged.connect(self._axis_slider_changed)
self.top_axis.line.valueChanged.connect(self._axis_slider_changed)
self.dendrogram.geometryChanged.connect(self._dendrogram_geom_changed)
self._set_cut_line_visible(self.selection_method == 1)
def __init__(self, parent=None):
super().__init__(self, parent)
self.clusterDataset = None
self.referenceDataset = None
self.ontology = None
self.annotations = None
self.loadedAnnotationCode = None
self.treeStructRootKey = None
self.probFunctions = [
statistics.Binomial(),
statistics.Hypergeometric()
]
self.selectedTerms = []
self.selectionChanging = 0
self.__state = State.Ready
self.__scheduletimer = QTimer(self, singleShot=True)
self.__scheduletimer.timeout.connect(self.__update)
#############
# GUI
#############
self.tabs = gui.tabWidget(self.controlArea)
# Input tab
self.inputTab = gui.createTabPage(self.tabs, "Input")
box = gui.widgetBox(self.inputTab, "Info")
self.infoLabel = gui.widgetLabel(box, "No data on input\n")
gui.button(
box,
self,
"Ontology/Annotation Info",
callback=self.ShowInfo,
tooltip="Show information on loaded ontology and annotations")
box = gui.widgetBox(self.inputTab, "Organism")
self.annotationComboBox = gui.comboBox(
box,
self,
"annotationIndex",
items=[],
callback=self.__invalidateAnnotations,
tooltip="Select organism")
genebox = gui.widgetBox(self.inputTab, "Gene Names")
self.geneAttrIndexCombo = gui.comboBox(
genebox,
self,
"geneAttrIndex",
callback=self.__invalidate,
tooltip="Use this attribute to extract gene names from input data")
self.geneAttrIndexCombo.setDisabled(self.useAttrNames)
self.useAttrNames_checkbox = gui.checkBox(
genebox,
self,
"useAttrNames",
"Use column names",
tooltip="Use column names for gene names",
callback=self.__invalidate)
self.useAttrNames_checkbox.toggled[bool].connect(
self.geneAttrIndexCombo.setDisabled)
self.referenceRadioBox = gui.radioButtonsInBox(
self.inputTab,
self,
"useReferenceDataset", ["Entire genome", "Reference set (input)"],
tooltips=[
"Use entire genome for reference",
"Use genes from Referece Examples input signal as reference"
],
box="Reference",
callback=self.__invalidate)
self.referenceRadioBox.buttons[1].setDisabled(True)
gui.radioButtonsInBox(
self.inputTab,
self,
"aspectIndex",
["Biological process", "Cellular component", "Molecular function"],
box="Aspect",
callback=self.__invalidate)
# Filter tab
self.filterTab = gui.createTabPage(self.tabs, "Filter")
box = gui.widgetBox(self.filterTab, "Filter GO Term Nodes")
gui.checkBox(
box,
self,
"filterByNumOfInstances",
"Genes",
callback=self.FilterAndDisplayGraph,
tooltip="Filter by number of input genes mapped to a term")
ibox = gui.indentedBox(box)
gui.spin(ibox,
self,
'minNumOfInstances',
1,
100,
step=1,
label='#:',
labelWidth=15,
callback=self.FilterAndDisplayGraph,
callbackOnReturn=True,
tooltip="Min. number of input genes mapped to a term")
gui.checkBox(box,
self,
"filterByPValue_nofdr",
"p-value",
callback=self.FilterAndDisplayGraph,
tooltip="Filter by term p-value")
gui.doubleSpin(gui.indentedBox(box),
self,
'maxPValue_nofdr',
1e-8,
1,
step=1e-8,
label='p:',
labelWidth=15,
callback=self.FilterAndDisplayGraph,
callbackOnReturn=True,
tooltip="Max term p-value")
# use filterByPValue for FDR, as it was the default in prior versions
gui.checkBox(box,
self,
"filterByPValue",
"FDR",
callback=self.FilterAndDisplayGraph,
tooltip="Filter by term FDR")
gui.doubleSpin(gui.indentedBox(box),
self,
'maxPValue',
1e-8,
1,
step=1e-8,
label='p:',
labelWidth=15,
callback=self.FilterAndDisplayGraph,
callbackOnReturn=True,
tooltip="Max term p-value")
box = gui.widgetBox(box, "Significance test")
gui.radioButtonsInBox(
box,
self,
"probFunc", ["Binomial", "Hypergeometric"],
tooltips=[
"Use binomial distribution test",
"Use hypergeometric distribution test"
],
callback=self.__invalidate) # TODO: only update the p values
box = gui.widgetBox(self.filterTab,
"Evidence codes in annotation",
addSpace=True)
self.evidenceCheckBoxDict = {}
for etype in go.evidenceTypesOrdered:
ecb = QCheckBox(etype,
toolTip=go.evidenceTypes[etype],
checked=self.useEvidenceType[etype])
ecb.toggled.connect(self.__on_evidenceChanged)
box.layout().addWidget(ecb)
self.evidenceCheckBoxDict[etype] = ecb
# Select tab
self.selectTab = gui.createTabPage(self.tabs, "Select")
box = gui.radioButtonsInBox(self.selectTab,
self,
"selectionDirectAnnotation",
["Directly or Indirectly", "Directly"],
box="Annotated genes",
callback=self.ExampleSelection)
box = gui.widgetBox(self.selectTab, "Output", addSpace=True)
gui.radioButtonsInBox(
box,
self,
"selectionDisjoint",
btnLabels=[
"All selected genes", "Term-specific genes",
"Common term genes"
],
tooltips=[
"Outputs genes annotated to all selected GO terms",
"Outputs genes that appear in only one of selected GO terms",
"Outputs genes common to all selected GO terms"
],
callback=[self.ExampleSelection, self.UpdateAddClassButton])
self.addClassCB = gui.checkBox(box,
self,
"selectionAddTermAsClass",
"Add GO Term as class",
callback=self.ExampleSelection)
# ListView for DAG, and table for significant GOIDs
self.DAGcolumns = [
'GO term', 'Cluster', 'Reference', 'p-value', 'FDR', 'Genes',
'Enrichment'
]
self.splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitter)
# list view
self.listView = GOTreeWidget(self.splitter)
self.listView.setSelectionMode(QTreeView.ExtendedSelection)
self.listView.setAllColumnsShowFocus(1)
self.listView.setColumnCount(len(self.DAGcolumns))
self.listView.setHeaderLabels(self.DAGcolumns)
self.listView.header().setSectionsClickable(True)
self.listView.header().setSortIndicatorShown(True)
self.listView.header().setSortIndicator(
self.DAGcolumns.index('p-value'), Qt.DescendingOrder)
self.listView.setSortingEnabled(True)
self.listView.setItemDelegateForColumn(
6, EnrichmentColumnItemDelegate(self))
self.listView.setRootIsDecorated(True)
self.listView.itemSelectionChanged.connect(self.ViewSelectionChanged)
# table of significant GO terms
self.sigTerms = QTreeWidget(self.splitter)
self.sigTerms.setColumnCount(len(self.DAGcolumns))
self.sigTerms.setHeaderLabels(self.DAGcolumns)
self.sigTerms.setSortingEnabled(True)
self.sigTerms.setSelectionMode(QTreeView.ExtendedSelection)
self.sigTerms.header().setSortIndicator(
self.DAGcolumns.index('p-value'), Qt.DescendingOrder)
self.sigTerms.setItemDelegateForColumn(
6, EnrichmentColumnItemDelegate(self))
self.sigTerms.itemSelectionChanged.connect(self.TableSelectionChanged)
self.sigTableTermsSorted = []
self.graph = {}
self.originalGraph = None
self.inputTab.layout().addStretch(1)
self.filterTab.layout().addStretch(1)
self.selectTab.layout().addStretch(1)
class AnnotationSlot(SimpleNamespace):
taxid = ... # type: str
name = ... # type: str
filename = ... # type:str
@staticmethod
def parse_tax_id(f_name):
return f_name.split('.')[1]
available_annotations = [
AnnotationSlot(taxid=AnnotationSlot.parse_tax_id(annotation_file),
name=taxonomy.common_taxid_to_name(
AnnotationSlot.parse_tax_id(annotation_file)),
filename=FILENAME_ANNOTATION.format(
AnnotationSlot.parse_tax_id(annotation_file)))
for _, annotation_file in serverfiles.ServerFiles().listfiles(
DOMAIN) if annotation_file != FILENAME_ONTOLOGY
]
self.availableAnnotations = sorted(available_annotations,
key=lambda a: a.name)
self.annotationComboBox.clear()
for a in self.availableAnnotations:
self.annotationComboBox.addItem(a.name)
self.annotationComboBox.setCurrentIndex(self.annotationIndex)
self.annotationIndex = self.annotationComboBox.currentIndex()
self._executor = ThreadExecutor()
def __init__(self):
super().__init__()
self.controlArea = QWidget(self.controlArea)
self.layout().addWidget(self.controlArea)
layout = QGridLayout()
self.controlArea.setLayout(layout)
layout.setContentsMargins(4, 4, 4, 4)
self.methods = [
("number_of_nodes", True, "Number of nodes", GRAPHLEVEL, lambda G: G.number_of_nodes()),
("number_of_edges", True, "Number of edges", GRAPHLEVEL, lambda G: G.number_of_edges()),
("average_degree", True, "Average degree", GRAPHLEVEL, lambda G: np.average(list(G.degree().values()))),
("diameter", False, "Diameter", GRAPHLEVEL, nx.diameter),
("radius", False, "Radius", GRAPHLEVEL, nx.radius),
("average_shortest_path_length", False, "Average shortest path length", GRAPHLEVEL, nx.average_shortest_path_length),
("density", True, "Density", GRAPHLEVEL, nx.density),
("degree_assortativity_coefficient", False, \
"Degree assortativity coefficient", GRAPHLEVEL, \
nx.degree_assortativity_coefficient if \
hasattr(nx, "degree_assortativity_coefficient") else None),
# additional attr needed
#("attribute_assortativity_coefficient", False, "Attribute assortativity coefficient", GRAPHLEVEL, nx.attribute_assortativity_coefficient),
#("numeric_assortativity_coefficient", False, "Numeric assortativity coefficient", GRAPHLEVEL, nx.numeric_assortativity_coefficient),
("degree_pearson_correlation_coefficient", False, \
"Degree pearson correlation coefficient", GRAPHLEVEL, \
nx.degree_pearson_correlation_coefficient if\
hasattr(nx, "degree_pearson_correlation_coefficient") else None),
("estrada_index", False, "Estrada index", GRAPHLEVEL, \
nx.estrada_index if hasattr(nx, "estrada_index") else None),
("graph_clique_number", False, "Graph clique number", GRAPHLEVEL, nx.graph_clique_number),
("graph_number_of_cliques", False, "Graph number of cliques", GRAPHLEVEL, nx.graph_number_of_cliques),
("transitivity", False, "Graph transitivity", GRAPHLEVEL, nx.transitivity),
("average_clustering", False, "Average clustering coefficient", GRAPHLEVEL, nx.average_clustering),
("number_connected_components", False, "Number of connected components", GRAPHLEVEL, nx.number_connected_components),
("number_strongly_connected_components", False, "Number of strongly connected components", GRAPHLEVEL, nx.number_strongly_connected_components),
("number_weakly_connected_components", False, "Number of weakly connected components", GRAPHLEVEL, nx.number_weakly_connected_components),
("number_attracting_components", False, "Number of attracting components", GRAPHLEVEL, nx.number_attracting_components),
# TODO: input parameters
#("max_flow", False, "Maximum flow", GRAPHLEVEL, nx.max_flow),
#("min_cut", False, "Minimum cut", GRAPHLEVEL, nx.min_cut),
#("ford_fulkerson", False, "Maximum single-commodity flow (Ford-Fulkerson)", GRAPHLEVEL, nx.ford_fulkerson),
#("min_cost_flow_cost", False, "min_cost_flow_cost", GRAPHLEVEL, nx.min_cost_flow_cost),
# returns dict of dict
#("shortest_path_length", False, "Shortest path length", GRAPHLEVEL, nx.shortest_path_length),
("degree", False, "Degree", NODELEVEL, nx.degree),
("in_degree", False, "In-degree", NODELEVEL, lambda G: G.in_degree()),
("out_degree", False, "Out-degree", NODELEVEL, lambda G: G.out_degree()),
("average_neighbor_degree", False, "Average neighbor degree", NODELEVEL, nx.average_neighbor_degree),
("clustering", False, "Clustering coefficient", NODELEVEL, nx.clustering),
("triangles", False, "Number of triangles", NODELEVEL, nx.triangles),
("square_clustering", False, "Squares clustering coefficient", NODELEVEL, nx.square_clustering),
("number_of_cliques", False, "Number of cliques", NODELEVEL, nx.number_of_cliques),
("degree_centrality", False, "Degree centrality", NODELEVEL, nx.degree_centrality),
("in_degree_centrality", False, "In-egree centrality", NODELEVEL, nx.in_degree_centrality),
("out_degree_centrality", False, "Out-degree centrality", NODELEVEL, nx.out_degree_centrality),
("closeness_centrality", False, "Closeness centrality", NODELEVEL, nx.closeness_centrality),
("betweenness_centrality", False, "Betweenness centrality", NODELEVEL, nx.betweenness_centrality),
("current_flow_closeness_centrality", False, "Information centrality", NODELEVEL, nx.current_flow_closeness_centrality),
("current_flow_betweenness_centrality", False, "Random-walk betweenness centrality", NODELEVEL, nx.current_flow_betweenness_centrality),
("approximate_current_flow_betweenness_centrality", False, \
"Approx. random-walk betweenness centrality", NODELEVEL, \
nx.approximate_current_flow_betweenness_centrality if \
hasattr(nx, "approximate_current_flow_betweenness_centrality") \
else None),
("eigenvector_centrality", False, "Eigenvector centrality", NODELEVEL, nx.eigenvector_centrality),
("eigenvector_centrality_numpy", False, "Eigenvector centrality (NumPy)", NODELEVEL, nx.eigenvector_centrality_numpy),
("load_centrality", False, "Load centrality", NODELEVEL, nx.load_centrality),
("core_number", False, "Core number", NODELEVEL, nx.core_number),
("eccentricity", False, "Eccentricity", NODELEVEL, nx.eccentricity),
("closeness_vitality", False, "Closeness vitality", NODELEVEL, nx.closeness_vitality),
]
"""
TODO: add
average-degree_connectivity
is_bipartite
is_chordal
katz_centrality
katz_centrality_numpy
communicability
communicability_exp
communicability_centrality
communicability_centrality_exp
communicability_betweenness_centrality
average_node_connectivity
is_directed_acyclic_graph
center
??
"""
self.methods = [method for method in self.methods if method[-1] is not None]
self.tab_index = 0
self.mutex = QMutex()
self.graph = None
self.items = None # items set by Items signal
self.items_graph = None # items set by graph.items by Network signal
self.items_analysis = None # items to output and merge with analysis result
self.job_queue = []
self.job_working = []
self.analfeatures = []
self.analdata = {}
for method in self.methods:
setattr(self, method[0], method[1])
setattr(self, "lbl_" + method[0], "")
self.tabs = gui.tabWidget(self.controlArea)
self.tabs.setMinimumWidth(450)
self.graphIndices = gui.createTabPage(self.tabs, "Graph-level indices")
self.nodeIndices = gui.createTabPage(self.tabs, "Node-level indices")
self.tabs.setCurrentIndex(self.tab_index)
self.tabs.currentChanged.connect(lambda index: setattr(self, 'tab_index', index))
for name, default, label, type, algorithm in self.methods:
if type == NODELEVEL:
box = gui.widgetBox(self.nodeIndices, orientation="horizontal")
elif type == GRAPHLEVEL:
box = gui.widgetBox(self.graphIndices, orientation="horizontal")
gui.checkBox(box, self, name, label=label, callback=lambda n=name: self.method_clicked(n))
box.layout().addStretch(1)
lbl = gui.label(box, self, "%(lbl_" + name + ")s")
setattr(self, "tool_" + name, lbl)
self.graphIndices.layout().addStretch(1)
self.nodeIndices.layout().addStretch(1)
autobox = gui.auto_commit(None, self, "auto_commit", "Commit", commit=self.analyze)
layout.addWidget(autobox, 3, 0, 1, 1)
cancel = gui.button(None, self, "Cancel", callback=lambda: self.stop_job(current=False))
autobox.layout().insertWidget(3, cancel)
autobox.layout().insertSpacing(2, 10)
cancel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Preferred)
def __init__(self):
super().__init__()
self.old_purge_classes = True
self.conditions = []
self.last_output_conditions = None
self.data = None
self.data_desc = self.match_desc = self.nonmatch_desc = None
box = gui.vBox(self.controlArea, 'Conditions', stretch=100)
self.cond_list = QTableWidget(box,
showGrid=False,
selectionMode=QTableWidget.NoSelection)
box.layout().addWidget(self.cond_list)
self.cond_list.setColumnCount(4)
self.cond_list.setRowCount(0)
self.cond_list.verticalHeader().hide()
self.cond_list.horizontalHeader().hide()
for i in range(3):
self.cond_list.horizontalHeader().setSectionResizeMode(
i, QHeaderView.Stretch)
self.cond_list.horizontalHeader().resizeSection(3, 30)
self.cond_list.viewport().setBackgroundRole(QPalette.Window)
box2 = gui.hBox(box)
gui.rubber(box2)
self.add_button = gui.button(box2,
self,
"Add Condition",
callback=self.add_row)
self.add_all_button = gui.button(box2,
self,
"Add All Variables",
callback=self.add_all)
self.remove_all_button = gui.button(box2,
self,
"Remove All",
callback=self.remove_all)
gui.rubber(box2)
boxes = gui.widgetBox(self.controlArea, orientation=QGridLayout())
layout = boxes.layout()
layout.setColumnStretch(0, 1)
layout.setColumnStretch(1, 1)
box_data = gui.vBox(boxes, 'Data', addToLayout=False)
self.data_in_variables = gui.widgetLabel(box_data, " ")
self.data_out_rows = gui.widgetLabel(box_data, " ")
layout.addWidget(box_data, 0, 0)
box_setting = gui.vBox(boxes, 'Purging', addToLayout=False)
self.cb_pa = gui.checkBox(box_setting,
self,
"purge_attributes",
"Remove unused features",
callback=self.conditions_changed)
gui.separator(box_setting, height=1)
self.cb_pc = gui.checkBox(box_setting,
self,
"purge_classes",
"Remove unused classes",
callback=self.conditions_changed)
layout.addWidget(box_setting, 0, 1)
self.report_button.setFixedWidth(120)
gui.rubber(self.buttonsArea.layout())
layout.addWidget(self.buttonsArea, 1, 0)
acbox = gui.auto_commit(None,
self,
"auto_commit",
label="Send",
orientation=Qt.Horizontal,
checkbox_label="Send automatically")
layout.addWidget(acbox, 1, 1)
self.set_data(None)
self.resize(600, 400)
def __init__(self):
"""Widget creator."""
super().__init__()
# ATTRIBUTS
# searchFunction
self.searchResults = None
self.inputSeg = None
# newQuery = attribut box lineEdit (search something)
self.newQuery = ''
self.nbr_results = 10
# Results box attributs
self.titleLabels = list()
self.selectedTitles = list()
# selections box attributs
self.myTitles = list()
self.mytitleLabels = list()
# stock all the inputs (scripts) in a list
self.createdInputs = list()
self.path_storage = list()
# Next two instructions are helpers from TextableUtils. Corresponding
# interface elements are declared here and actually drawn below (at
# their position in the UI)...
self.infoBox = InfoBox(widget=self.controlArea)
#self.sendButton = SendButton(
# widget=self.controlArea,
# master=self,
# callback=self.sendData,
# infoBoxAttribute="infoBox",
#)
# User interface...
# Create the working area
queryBox = gui.widgetBox(
widget=self.controlArea,
box="Search movie",
orientation="vertical",
)
# Allows to enter specific text to the research
# Uses "newQuery" attribute
gui.lineEdit(
widget=queryBox,
master=self,
value='newQuery',
orientation='horizontal',
label=u"Movie title: ",
labelWidth=100,
tooltip=("Enter a string"),
)
# Allows to choose the wanted results numberp (10 by 10)
queryNbr = gui.comboBox(
widget=queryBox,
master=self,
value="nbr_results",
items=[
"5",
"10",
"20",
"30",
"40",
"50",
],
sendSelectedValue=True,
orientation="horizontal",
label="Number of results: ",
labelWidth=120,
tooltip=("Please select the desired search.\n"),
)
# Research button
# Use "searchFunction" attibute
self.searchButton = gui.button(
widget=queryBox,
master=self,
label='Search',
callback=self.searchFunction,
tooltip='Search for the movie',
)
# Reasearch button
# Uses "searchFunction" attribute
self.titleListbox = gui.listBox(
widget=queryBox,
master=self,
value="selectedTitles", # setting (list)
labels="titleLabels", # setting (list)
callback=lambda: self.selectButton.setDisabled(self.selectedTitles
== list()),
tooltip="Select the movie you want to get the script of",
)
self.titleListbox.setMinimumHeight(120)
self.titleListbox.setSelectionMode(3)
boxbutton = gui.widgetBox(
widget=queryBox,
box=False,
orientation='horizontal',
)
# select button
# Uses "select" function
self.selectButton = gui.button(
widget=boxbutton,
master=self,
label="Select",
callback=self.sendData,
tooltip="Select",
)
self.selectButton.setDisabled(True)
# Clear button
# Uses "clearResults" function
self.clearButton = gui.button(
widget=boxbutton,
master=self,
label="Clear results",
callback=self.clearResults,
tooltip="Clear results",
)
self.clearButton.setDisabled(True)
gui.separator(widget=queryBox, height=3)
gui.rubber(self.controlArea)
#----------------------------------------------------------------------
# Draw Info box and Send button
# self.sendButton.draw()
# self.searchButton.setDefault(True)
self.infoBox.draw()
def __init__(self, parent=None):
widget.OWWidget.__init__(self, parent)
self.min_value, self.max_value = \
self.thresholds.get(self.Scores[self.score_index][0], (1, 0))
#: Input data set
self.data = None
#: Current target group selection
self.targets = []
#: The computed scores
self.scores = None
#: The computed scores from label permutations
self.nulldist = None
self.__scores_future = self.__scores_state = None
self.__in_progress = False
self.test_f = {
OWDifferentialExpression.LowTail: test_low,
OWDifferentialExpression.HighTail: test_high,
OWDifferentialExpression.TwoTail: test_two_tail,
}
self.histogram = Histogram(enableMouse=False,
enableMenu=False,
background="w")
self.histogram.enableAutoRange(enable=False)
self.histogram.getPlotItem().hideButtons() # hide auto range button
self.histogram.getViewBox().setMouseEnabled(False, False)
self.histogram.selectionChanged.connect(
self.__on_histogram_plot_selection_changed)
self.histogram.selectionEdited.connect(self._invalidate_selection)
self.mainArea.layout().addWidget(self.histogram)
box = gui.widgetBox(self.controlArea, "Info")
self.dataInfoLabel = gui.widgetLabel(box, "No data on input.\n")
self.dataInfoLabel.setWordWrap(True)
self.selectedInfoLabel = gui.widgetLabel(box, "\n")
box1 = gui.widgetBox(self.controlArea, "Scoring Method")
gui.comboBox(
box1,
self,
"score_index",
items=[sm[0] for sm in self.Scores],
callback=[self.on_scoring_method_changed, self.update_scores])
box = gui.widgetBox(self.controlArea, "Target Labels")
self.label_selection_widget = guiutils.LabelSelectionWidget(self)
self.label_selection_widget.setMaximumHeight(150)
box.layout().addWidget(self.label_selection_widget)
self.label_selection_widget.groupChanged.connect(
self.on_label_activated)
self.label_selection_widget.groupSelectionChanged.connect(
self.on_target_changed)
box = gui.widgetBox(self.controlArea, "Selection")
box.layout().setSpacing(0)
self.max_value_spin = gui.doubleSpin(box,
self,
"max_value",
minv=-1e6,
maxv=1e6,
step=1e-6,
label="Upper threshold:",
callback=self.update_boundary,
callbackOnReturn=True)
self.low_value_spin = gui.doubleSpin(box,
self,
"min_value",
minv=-1e6,
maxv=1e6,
step=1e-6,
label="Lower threshold:",
callback=self.update_boundary,
callbackOnReturn=True)
check = gui.checkBox(box,
self,
"compute_null",
"Compute null distribution",
callback=self.update_scores)
perm_spin = gui.spin(box,
self,
"permutations_count",
minv=1,
maxv=50,
label="Permutations:",
callback=self.update_scores,
callbackOnReturn=True)
check.disables.append(perm_spin)
box1 = gui.widgetBox(box, orientation='horizontal')
pval_spin = gui.doubleSpin(box1,
self,
"alpha_value",
minv=2e-7,
maxv=1.0,
step=1e-7,
label="α-value:")
pval_select = gui.button(box1,
self,
"Select",
callback=self.select_p_best,
autoDefault=False)
check.disables.append(pval_spin)
check.disables.append(pval_select)
check.makeConsistent()
box1 = gui.widgetBox(box, orientation='horizontal')
gui.spin(box1, self, "n_best", 0, 10000, step=1, label="Best Ranked:")
gui.button(box1,
self,
"Select",
callback=self.select_n_best,
autoDefault=False)
box = gui.widgetBox(self.controlArea, "Output")
acbox = gui.auto_commit(box, self, "auto_commit", "Commit", box=None)
acbox.button.setDefault(True)
gui.checkBox(box,
self,
"add_scores_to_output",
"Add gene scores to output",
callback=self._invalidate_selection)
gui.rubber(self.controlArea)
self.on_scoring_method_changed()
self._executor = concurrent.ThreadExecutor()
def __init__(self, *args, **kwargs):
"""Initialize a Message widget"""
super().__init__(*args, **kwargs)
# Other attributes...
self.segmentation = None
self.createdInputs = list()
self.noLanguageParameterWarning = (
"Please make sure that at least one language parameter "
"file is installed in your Treetagger 'lib' directory, "
"then click 'Reload language parameter files'."
)
self.noTreetaggerPathWarning = (
"Please click 'Locate Treetagger' below and select the "
"base directory of a valid Treetagger distribution."
)
self.TreetaggerPath = (
treetaggerwrapper.locate_treetagger() or
self.lookupSavedTreetaggerPath()
)
self.infoBox = InfoBox(widget=self.controlArea)
self.sendButton = SendButton(
widget=self.controlArea,
master=self,
callback=self.sendData,
infoBoxAttribute=u"infoBox",
sendIfPreCallback=self.updateGUI
)
gui.separator(self.controlArea, height=3)
self.optionsBox = gui.widgetBox(
self.controlArea,
u"Options",
)
self.languageCombobox = gui.comboBox(
widget=self.optionsBox,
master=self,
value="language",
items=list(),
sendSelectedValue=True,
orientation=u"horizontal",
label="Input language:",
labelWidth=180,
callback=self.sendButton.settingsChanged,
tooltip=(
u"Select the language of the input text."
),
)
self.languageCombobox.setMinimumWidth(120)
gui.separator(self.optionsBox, height=3)
gui.comboBox(
widget=self.optionsBox,
master=self,
value="outputFormat",
items=[
"segment into words",
"add XML tags",
],
sendSelectedValue=True,
orientation=u"horizontal",
label="Output format:",
labelWidth=180,
callback=self.sendButton.settingsChanged,
tooltip=(
u"Select the format of the output:\n\n"
u"Segment into words: each word is in a separate segment,\n"
u"with lemma and POS-tag as annotations.\n\n"
u"Add XML tags: output segments correspond to input segments\n"
u"and each word is tagged in XML as a 'w' element with\n"
u"lemma and POS-tag as attributes."
),
)
gui.separator(self.optionsBox, height=3)
gui.checkBox(
widget=self.optionsBox,
master=self,
value="replaceUnknown",
label="Output token in place of [unknown] lemmas",
callback=self.sendButton.settingsChanged,
tooltip=(
u"For out-of-vocabulary words, the word form is used as the\n"
u"lemma (in place of Treetagger's default 'unknown' code)."
),
)
gui.rubber(self.controlArea)
self.sendButton.draw()
self.infoBox.draw()
self.locateTreetaggerBox=gui.widgetBox(
self.controlArea,
addSpace=False,
)
gui.separator(self.locateTreetaggerBox, height=3)
self.treetaggerButton = gui.button(
widget=self.locateTreetaggerBox,
master=self,
label="Locate Treetagger",
callback=self.validateTreetagger,
tooltip=(
u"Click to select the location of the Treetagger base\n"
u"directory (containing the 'lib' and 'bin' subdirectories)."
),
)
self.sendButton.sendIf()
self.adjustSizeWithTimer()
def __init__(self):
super().__init__()
self.controlArea = QtGui.QWidget(self.leftWidgetPart)
self.layout().addWidget(self.controlArea)
layout = QtGui.QGridLayout()
self.controlArea.setLayout(layout)
layout.setMargin(4)
box = gui.widgetBox(self.controlArea,
"Available Variables",
addToLayout=False)
self.filter_edit = QtGui.QLineEdit()
self.filter_edit.setToolTip("Filter the list of available variables.")
box.layout().addWidget(self.filter_edit)
if hasattr(self.filter_edit, "setPlaceholderText"):
self.filter_edit.setPlaceholderText("Filter")
self.completer = QtGui.QCompleter()
self.completer.setCompletionMode(QtGui.QCompleter.InlineCompletion)
self.completer_model = QtGui.QStringListModel()
self.completer.setModel(self.completer_model)
self.completer.setModelSorting(
QtGui.QCompleter.CaseSensitivelySortedModel)
self.filter_edit.setCompleter(self.completer)
self.completer_navigator = CompleterNavigator(self)
self.filter_edit.installEventFilter(self.completer_navigator)
self.available_attrs = VariablesListItemModel()
self.available_attrs_proxy = VariableFilterProxyModel()
self.available_attrs_proxy.setSourceModel(self.available_attrs)
self.available_attrs_view = VariablesListItemView()
self.available_attrs_view.setModel(self.available_attrs_proxy)
aa = self.available_attrs
aa.dataChanged.connect(self.update_completer_model)
aa.rowsInserted.connect(self.update_completer_model)
aa.rowsRemoved.connect(self.update_completer_model)
self.available_attrs_view.selectionModel().selectionChanged.connect(
partial(self.update_interface_state, self.available_attrs_view))
self.filter_edit.textChanged.connect(self.update_completer_prefix)
self.filter_edit.textChanged.connect(
self.available_attrs_proxy.set_filter_string)
box.layout().addWidget(self.available_attrs_view)
layout.addWidget(box, 0, 0, 3, 1)
box = gui.widgetBox(self.controlArea, "Features", addToLayout=False)
self.used_attrs = VariablesListItemModel()
self.used_attrs_view = VariablesListItemView()
self.used_attrs_view.setModel(self.used_attrs)
self.used_attrs_view.selectionModel().selectionChanged.connect(
partial(self.update_interface_state, self.used_attrs_view))
box.layout().addWidget(self.used_attrs_view)
layout.addWidget(box, 0, 2, 1, 1)
box = gui.widgetBox(self.controlArea, "Class", addToLayout=False)
self.class_attrs = ClassVarListItemModel()
self.class_attrs_view = ClassVariableItemView()
self.class_attrs_view.setModel(self.class_attrs)
self.class_attrs_view.selectionModel().selectionChanged.connect(
partial(self.update_interface_state, self.class_attrs_view))
self.class_attrs_view.setMaximumHeight(24)
box.layout().addWidget(self.class_attrs_view)
layout.addWidget(box, 1, 2, 1, 1)
box = gui.widgetBox(self.controlArea,
"Meta Attributes",
addToLayout=False)
self.meta_attrs = VariablesListItemModel()
self.meta_attrs_view = VariablesListItemView()
self.meta_attrs_view.setModel(self.meta_attrs)
self.meta_attrs_view.selectionModel().selectionChanged.connect(
partial(self.update_interface_state, self.meta_attrs_view))
box.layout().addWidget(self.meta_attrs_view)
layout.addWidget(box, 2, 2, 1, 1)
bbox = gui.widgetBox(self.controlArea, addToLayout=False, margin=0)
layout.addWidget(bbox, 0, 1, 1, 1)
self.up_attr_button = gui.button(bbox,
self,
"Up",
callback=partial(
self.move_up,
self.used_attrs_view))
self.move_attr_button = gui.button(bbox,
self,
">",
callback=partial(
self.move_selected,
self.used_attrs_view))
self.down_attr_button = gui.button(bbox,
self,
"Down",
callback=partial(
self.move_down,
self.used_attrs_view))
bbox = gui.widgetBox(self.controlArea, addToLayout=False, margin=0)
layout.addWidget(bbox, 1, 1, 1, 1)
self.move_class_button = gui.button(bbox,
self,
">",
callback=partial(
self.move_selected,
self.class_attrs_view,
exclusive=True))
bbox = gui.widgetBox(self.controlArea, addToLayout=False, margin=0)
layout.addWidget(bbox, 2, 1, 1, 1)
self.up_meta_button = gui.button(bbox,
self,
"Up",
callback=partial(
self.move_up,
self.meta_attrs_view))
self.move_meta_button = gui.button(bbox,
self,
">",
callback=partial(
self.move_selected,
self.meta_attrs_view))
self.down_meta_button = gui.button(bbox,
self,
"Down",
callback=partial(
self.move_down,
self.meta_attrs_view))
bbox = gui.widgetBox(self.controlArea,
orientation="horizontal",
addToLayout=False,
margin=0)
gui.button(bbox, self, "Apply", callback=self.commit)
gui.button(bbox, self, "Reset", callback=self.reset)
layout.addWidget(bbox, 3, 0, 1, 3)
layout.setRowStretch(0, 4)
layout.setRowStretch(1, 0)
layout.setRowStretch(2, 2)
layout.setHorizontalSpacing(0)
self.controlArea.setLayout(layout)
self.data = None
self.output_report = None
self.original_completer_items = []
self.resize(500, 600)
# For automatic widget testing using
self._guiElements.extend([
(QtGui.QListView, self.available_attrs_view),
(QtGui.QListView, self.used_attrs_view),
(QtGui.QListView, self.class_attrs_view),
(QtGui.QListView, self.meta_attrs_view),
])
def _insert_buttons_area(self):
self.buttonsArea = gui.widgetBox(
self.left_side,
addSpace=0,
spacing=9,
orientation=self.buttons_area_orientation)
def __init__(self):
super().__init__()
self.domain = None
self.graph = None
self.auto_items = None
self.net_index = 0
self.data_index = 0
#GUI
self.controlArea.layout().setContentsMargins(4, 4, 4, 4)
self.box = gui.widgetBox(self.controlArea,
box="Graph File",
orientation="vertical")
hb = gui.widgetBox(self.box, orientation="horizontal")
self.filecombo = gui.comboBox(hb,
self,
"net_index",
callback=self.selectNetFile)
self.filecombo.setMinimumWidth(250)
button = gui.button(hb,
self,
'...',
callback=self.browseNetFile,
disabled=0)
button.setIcon(self.style().standardIcon(QStyle.SP_DirOpenIcon))
button.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Fixed)
button = gui.button(hb, self, 'Reload', callback=self.reload)
button.setIcon(self.style().standardIcon(QStyle.SP_BrowserReload))
chb = gui.widgetBox(self.box, orientation="horizontal")
gui.checkBox(chb,
self,
"auto_table",
"Build graph data table automatically",
callback=self.selectNetFile)
self.databox = gui.widgetBox(self.controlArea,
box="Vertices Data File",
orientation="vertical")
vdf = gui.widgetBox(self.databox, orientation="horizontal")
self.datacombo = gui.comboBox(vdf,
self,
"data_index",
callback=self.selectDataFile)
self.datacombo.setMinimumWidth(250)
button = gui.button(vdf,
self,
'...',
callback=self.browseDataFile,
disabled=0)
button.setIcon(self.style().standardIcon(QStyle.SP_DirOpenIcon))
button.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Fixed)
button = gui.button(vdf, self, 'Reload', callback=self.reload_data)
button.setIcon(self.style().standardIcon(QStyle.SP_BrowserReload))
# info
box = gui.widgetBox(self.controlArea, "Info")
self.info = gui.widgetLabel(box, 'No data loaded.')
gui.rubber(self.controlArea)
self.resize(150, 100)
self.populate_comboboxes()
self.reload()
def __init__(self):
super().__init__()
self.data = None
self.samplingBox = [None, None]
self.sampleSizeBox = [None, None]
self.cvBox = [None, None]
box = gui.widgetBox(self.controlArea, "Information")
self.dataInfoLabel = gui.widgetLabel(box, 'No data on input.')
self.outputInfoLabel = gui.widgetLabel(box, ' ')
form = QtGui.QFormLayout(
formAlignment=Qt.AlignLeft | Qt.AlignTop,
labelAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow)
box = gui.widgetBox(self.controlArea, "Options", orientation=form)
cb = gui.checkBox(box,
self,
"stratified",
"Stratified (if possible)",
callback=self.settingsChanged,
addToLayout=False)
form.addRow(cb, QtGui.QWidget())
cb = gui.checkBox(box,
self,
"useSeed",
"Random seed:",
callback=self.settingsChanged,
addToLayout=False)
spin = gui.spin(box,
self,
"seed",
minv=0,
maxv=2**31 - 1,
callback=self.settingsChanged,
addToLayout=False)
form.addRow(cb, spin)
box = gui.widgetBox(self.controlArea, self.tr("Sampling Type"))
sampling = gui.radioButtons(box,
self,
"samplingType",
callback=self.samplingTypeChanged)
gui.appendRadioButton(sampling, "Random Sampling:")
self.samplingBox[0] = ibox = gui.indentedBox(sampling)
ibox.setEnabled(self.samplingType == OWDataSampler.RandomSampling)
ibox = gui.radioButtons(ibox,
self,
"sampleSizeType",
callback=self.sampleSizeTypeChanged)
gui.checkBox(ibox,
self,
"replacement",
"With replacement",
callback=self.settingsChanged)
gui.appendRadioButton(ibox, "Sample size:")
self.sampleSizeSpin = gui.spin(gui.indentedBox(ibox),
self,
"sampleSizeNumber",
minv=1,
maxv=2**31 - 1,
callback=self.settingsChanged)
self.sampleSizeSpin.setEnabled(self.sampleSizeType == self.Fixed)
gui.appendRadioButton(ibox, "Sample proportions:")
self.sampleSizePercentageSlider = gui.hSlider(
gui.indentedBox(ibox),
self,
"sampleSizePercentage",
minValue=1,
maxValue=100,
ticks=10,
labelFormat="%d%%",
callback=self.settingsChanged)
self.sampleSizePercentageSlider.setEnabled(
self.sampleSizeType == self.Ratio)
self.sampleSizeBox = [
self.sampleSizeSpin, self.sampleSizePercentageSlider
]
gui.appendRadioButton(sampling, "Cross Validation:")
self.samplingBox[1] = ibox = gui.indentedBox(sampling, addSpace=True)
ibox.setEnabled(self.samplingType == OWDataSampler.CrossValidation)
form = QtGui.QFormLayout(
formAlignment=Qt.AlignLeft | Qt.AlignTop,
labelAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow)
bbox = gui.radioButtons(ibox,
self,
"cvType",
orientation=form,
callback=self.cvTypeChanged,
addSpace=True)
bbox.setContentsMargins(1, 1, 1, 1)
kfold_rb = gui.appendRadioButton(bbox,
"K-Fold:",
insertInto=None,
addToLayout=False)
loo_rb = gui.appendRadioButton(bbox,
"Leave one out",
insertInto=None,
addToLayout=False)
kfold_spin = gui.spin(ibox,
self,
"numberOfFolds",
2,
100,
addToLayout=False,
callback=self.numberOfFoldsChanged)
kfold_spin.setEnabled(self.cvType == self.KFold)
form.addRow(kfold_rb, kfold_spin)
form.addRow(loo_rb)
self.cvBox = [kfold_spin]
self.selectedFoldSpin = gui.spin(ibox,
self,
"selectedFold",
1,
100,
addToLayout=False)
form.addRow(QtGui.QLabel("Selected fold:"), self.selectedFoldSpin)
gui.button(self.controlArea, self, "Sample Data", callback=self.commit)
def __init__(self):
super().__init__()
self.primary_data = None
self.more_data = OrderedDict()
mergebox = gui.widgetBox(self.controlArea, "Domains merging")
box = gui.radioButtons(mergebox,
self,
"merge_type",
callback=self._merge_type_changed)
gui.widgetLabel(
box,
self.tr("When there is no primary table, " +
"the domain should be:"))
for opts in self.domain_opts:
gui.appendRadioButton(box, self.tr(opts))
gui.separator(box)
label = gui.widgetLabel(
box,
self.tr("The resulting table will have class only if there " +
"is no conflict between input classes."))
label.setWordWrap(True)
###
box = gui.widgetBox(self.controlArea,
self.tr("Source identification"),
addSpace=False)
cb = gui.checkBox(box, self, "append_source_column",
self.tr("Append data source IDs"))
ibox = gui.indentedBox(box, sep=gui.checkButtonOffsetHint(cb))
form = QtGui.QFormLayout(
spacing=8,
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow)
form.addRow(
self.tr("Feature name"),
gui.lineEdit(ibox, self, "source_attr_name", valueType=str))
form.addRow(
self.tr("Place"),
gui.comboBox(ibox, self, "source_column_role",
items=self.id_roles))
ibox.layout().addLayout(form)
mleft, mtop, mright, _ = ibox.layout().getContentsMargins()
ibox.layout().setContentsMargins(mleft, mtop, mright, 4)
cb.disables.append(ibox)
cb.makeConsistent()
gui.separator(self.controlArea, 8)
box = gui.widgetBox(
self.controlArea,
True,
orientation="horizontal",
)
box.layout().addWidget(self.report_button)
gui.separator(box, 20)
gui.button(box,
self,
self.tr("Apply Changes"),
callback=self.apply,
default=True)
def __init__(self):
super().__init__()
RecentPathsWComboMixin.__init__(self)
self.domain = None
self.data = None
self.loaded_file = ""
self.reader = None
layout = QtGui.QGridLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
vbox = gui.radioButtons(None,
self,
"source",
box=True,
addSpace=True,
callback=self.load_data,
addToLayout=False)
rb_button = gui.appendRadioButton(vbox, "File:", addToLayout=False)
layout.addWidget(rb_button, 0, 0, QtCore.Qt.AlignVCenter)
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.file_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.file_combo.activated[int].connect(self.select_file)
box.layout().addWidget(self.file_combo)
layout.addWidget(box, 0, 1)
file_button = gui.button(None,
self,
'...',
callback=self.browse_file,
autoDefault=False)
file_button.setIcon(self.style().standardIcon(
QtGui.QStyle.SP_DirOpenIcon))
file_button.setSizePolicy(Policy.Maximum, Policy.Fixed)
layout.addWidget(file_button, 0, 2)
reload_button = gui.button(None,
self,
"Reload",
callback=self.load_data,
autoDefault=False)
reload_button.setIcon(self.style().standardIcon(
QtGui.QStyle.SP_BrowserReload))
reload_button.setSizePolicy(Policy.Fixed, Policy.Fixed)
layout.addWidget(reload_button, 0, 3)
self.sheet_box = gui.hBox(None, addToLayout=False, margin=0)
self.sheet_combo = gui.comboBox(None,
self,
"xls_sheet",
callback=self.select_sheet,
sendSelectedValue=True)
self.sheet_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_label = QtGui.QLabel()
self.sheet_label.setText('Sheet')
self.sheet_label.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_box.layout().addWidget(self.sheet_label,
QtCore.Qt.AlignLeft)
self.sheet_box.layout().addWidget(self.sheet_combo,
QtCore.Qt.AlignVCenter)
layout.addWidget(self.sheet_box, 2, 1)
self.sheet_box.hide()
rb_button = gui.appendRadioButton(vbox, "URL:", addToLayout=False)
layout.addWidget(rb_button, 3, 0, QtCore.Qt.AlignVCenter)
self.url_combo = url_combo = QtGui.QComboBox()
url_model = NamedURLModel(self.sheet_names)
url_model.wrap(self.recent_urls)
url_combo.setModel(url_model)
url_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
url_combo.setEditable(True)
url_combo.setInsertPolicy(url_combo.InsertAtTop)
url_edit = url_combo.lineEdit()
l, t, r, b = url_edit.getTextMargins()
url_edit.setTextMargins(l + 5, t, r, b)
layout.addWidget(url_combo, 3, 1, 3, 3)
url_combo.activated.connect(self._url_set)
box = gui.vBox(self.controlArea, "Info")
self.info = gui.widgetLabel(box, 'No data loaded.')
self.warnings = gui.widgetLabel(box, '')
box = gui.widgetBox(self.controlArea, "Columns (Double click to edit)")
domain_editor = DomainEditor(self.variables)
self.editor_model = domain_editor.model()
box.layout().addWidget(domain_editor)
box = gui.hBox(self.controlArea)
gui.button(box,
self,
"Browse documentation data sets",
callback=lambda: self.browse_file(True),
autoDefault=False)
gui.rubber(box)
box.layout().addWidget(self.report_button)
self.report_button.setFixedWidth(170)
self.apply_button = gui.button(box,
self,
"Apply",
callback=self.apply_domain_edit)
self.apply_button.hide()
self.apply_button.setFixedWidth(170)
self.editor_model.dataChanged.connect(self.apply_button.show)
self.set_file_list()
# Must not call open_file from within __init__. open_file
# explicitly re-enters the event loop (by a progress bar)
QtCore.QTimer.singleShot(0, self.load_data)
self.setAcceptDrops(True)
def __init__(self):
super().__init__()
#: input data
self.data = None
self.class_var = None
#: Current variable discretization state
self.var_state = {}
#: Saved variable discretization settings (context setting)
self.saved_var_states = {}
self.method = 0
self.k = 5
self.cutpoints = []
box = gui.vBox(self.controlArea, self.tr("Default Discretization"))
self.default_bbox = rbox = gui.radioButtons(
box, self, "default_method", callback=self._default_disc_changed)
rb = gui.hBox(rbox)
self.left = gui.vBox(rb)
right = gui.vBox(rb)
rb.layout().setStretch(0, 1)
rb.layout().setStretch(1, 1)
options = self.options = [
self.tr("Default"),
self.tr("Leave numeric"),
self.tr("Entropy-MDL discretization"),
self.tr("Equal-frequency discretization"),
self.tr("Equal-width discretization"),
self.tr("Remove numeric variables")
]
for opt in options[1:]:
t = gui.appendRadioButton(rbox, opt)
# This condition is ugly, but it keeps the same order of
# options for backward compatibility of saved schemata
[right, self.left][opt.startswith("Equal")].layout().addWidget(t)
gui.separator(right, 18, 18)
def _intbox(parent, attr, callback):
box = gui.indentedBox(parent)
s = gui.spin(box,
self,
attr,
minv=2,
maxv=10,
label="Num. of intervals:",
callback=callback)
s.setMaximumWidth(60)
s.setAlignment(Qt.AlignRight)
gui.rubber(s.box)
return box.box
self.k_general = _intbox(self.left, "default_k",
self._default_disc_changed)
self.k_general.layout().setContentsMargins(0, 0, 0, 0)
vlayout = QHBoxLayout()
box = gui.widgetBox(self.controlArea,
"Individual Attribute Settings",
orientation=vlayout,
spacing=8)
# List view with all attributes
self.varview = QListView(
selectionMode=QListView.ExtendedSelection,
uniformItemSizes=True,
)
self.varview.setItemDelegate(DiscDelegate())
self.varmodel = itemmodels.VariableListModel()
self.varview.setModel(self.varmodel)
self.varview.selectionModel().selectionChanged.connect(
self._var_selection_changed)
vlayout.addWidget(self.varview)
# Controls for individual attr settings
self.bbox = controlbox = gui.radioButtons(
box, self, "method", callback=self._disc_method_changed)
vlayout.addWidget(controlbox)
for opt in options[:5]:
gui.appendRadioButton(controlbox, opt)
self.k_specific = _intbox(controlbox, "k", self._disc_method_changed)
gui.appendRadioButton(controlbox, "Remove attribute")
gui.rubber(controlbox)
controlbox.setEnabled(False)
self.controlbox = controlbox
box = gui.auto_apply(self.controlArea, self, "autosend")
box.button.setFixedWidth(180)
box.layout().insertStretch(0)
self._update_spin_positions()
self.info.set_input_summary(self.info.NoInput)
self.info.set_output_summary(self.info.NoOutput)
def __init__(self):
super().__init__()
self.corpus = None # Corpus
self.corpus_docs = None # Documents generated from Corpus
self.doc_webview = None # WebView for showing content
self.search_features = [] # two copies are needed since Display allows drag & drop
self.display_list_indices = [0]
# Info attributes
self.update_info()
info_box = gui.widgetBox(self.controlArea, 'Info')
gui.label(info_box, self, 'Documents: %(n_documents)s')
gui.label(info_box, self, 'Preprocessed: %(is_preprocessed)s')
gui.label(info_box, self, ' ◦ Tokens: %(n_tokens)s')
gui.label(info_box, self, ' ◦ Types: %(n_types)s')
gui.label(info_box, self, 'POS tagged: %(is_pos_tagged)s')
gui.label(info_box, self, 'N-grams range: %(ngram_range)s')
gui.label(info_box, self, 'Matching: %(n_matching)s')
# Search features
self.search_listbox = gui.listBox(
self.controlArea, self, 'search_indices', 'search_features',
selectionMode=QListView.ExtendedSelection,
box='Search features', callback=self.search_features_changed)
# Display features
display_box = gui.widgetBox(self.controlArea, 'Display features')
self.display_listbox = gui.listBox(
display_box, self, 'display_list_indices', 'display_features',
selectionMode=QListView.ExtendedSelection,
callback=self.show_docs, enableDragDrop=True)
self.show_tokens_checkbox = gui.checkBox(display_box, self, 'show_tokens',
'Show Tokens && Tags', callback=self.show_docs)
# Auto-commit box
gui.auto_commit(self.controlArea, self, 'autocommit', 'Send data', 'Auto send is on')
# Search
self.filter_input = gui.lineEdit(self.mainArea, self, 'regexp_filter',
orientation=Qt.Horizontal,
sizePolicy=QSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Fixed),
label='RegExp Filter:')
self.filter_input.textChanged.connect(self.refresh_search)
# Main area
self.splitter = QSplitter(
orientation=Qt.Horizontal,
childrenCollapsible=False,
)
# Document list
self.doc_list = QTableView()
self.doc_list.setSelectionBehavior(QTableView.SelectRows)
self.doc_list.setSelectionMode(QTableView.ExtendedSelection)
self.doc_list.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.doc_list.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.doc_list.horizontalHeader().setVisible(False)
self.splitter.addWidget(self.doc_list)
self.doc_list_model = QStandardItemModel(self)
self.doc_list.setModel(self.doc_list_model)
self.doc_list.selectionModel().selectionChanged.connect(
self.selection_changed
)
# Document contents
self.doc_webview = gui.WebviewWidget(self.splitter, debug=False)
self.mainArea.layout().addWidget(self.splitter)
def __init__(self):
super().__init__()
self.data = None # type: Optional[Table]
self.clusterings = {}
self.__executor = ThreadExecutor(parent=self)
self.__task = None # type: Optional[Task]
layout = QGridLayout()
bg = gui.radioButtonsInBox(
self.controlArea, self, "optimize_k", orientation=layout,
box="Number of Clusters", callback=self.update_method,
)
layout.addWidget(
gui.appendRadioButton(bg, "Fixed:", addToLayout=False), 1, 1)
sb = gui.hBox(None, margin=0)
gui.spin(
sb, self, "k", minv=2, maxv=30,
controlWidth=60, alignment=Qt.AlignRight, callback=self.update_k)
gui.rubber(sb)
layout.addWidget(sb, 1, 2)
layout.addWidget(
gui.appendRadioButton(bg, "From", addToLayout=False), 2, 1)
ftobox = gui.hBox(None)
ftobox.layout().setContentsMargins(0, 0, 0, 0)
layout.addWidget(ftobox, 2, 2)
gui.spin(
ftobox, self, "k_from", minv=2, maxv=29,
controlWidth=60, alignment=Qt.AlignRight,
callback=self.update_from)
gui.widgetLabel(ftobox, "to")
gui.spin(
ftobox, self, "k_to", minv=3, maxv=30,
controlWidth=60, alignment=Qt.AlignRight,
callback=self.update_to)
gui.rubber(ftobox)
box = gui.vBox(self.controlArea, "Initialization")
gui.comboBox(
box, self, "smart_init", items=[m[0] for m in self.INIT_METHODS],
callback=self.invalidate)
layout = QGridLayout()
gui.widgetBox(box, orientation=layout)
layout.addWidget(gui.widgetLabel(None, "Re-runs: "), 0, 0, Qt.AlignLeft)
sb = gui.hBox(None, margin=0)
layout.addWidget(sb, 0, 1)
gui.lineEdit(
sb, self, "n_init", controlWidth=60,
valueType=int, validator=QIntValidator(), callback=self.invalidate)
layout.addWidget(
gui.widgetLabel(None, "Maximum iterations: "), 1, 0, Qt.AlignLeft)
sb = gui.hBox(None, margin=0)
layout.addWidget(sb, 1, 1)
gui.lineEdit(
sb, self, "max_iterations", controlWidth=60, valueType=int,
validator=QIntValidator(), callback=self.invalidate)
self.apply_button = gui.auto_commit(
self.buttonsArea, self, "auto_commit", "Apply", box=None,
commit=self.commit)
gui.rubber(self.controlArea)
box = gui.vBox(self.mainArea, box="Silhouette Scores")
self.mainArea.setVisible(self.optimize_k)
self.table_model = ClusterTableModel(self)
table = self.table_view = QTableView(self.mainArea)
table.setModel(self.table_model)
table.setSelectionMode(QTableView.SingleSelection)
table.setSelectionBehavior(QTableView.SelectRows)
table.setItemDelegate(gui.ColoredBarItemDelegate(self, color=Qt.cyan))
table.selectionModel().selectionChanged.connect(self.select_row)
table.setMaximumWidth(200)
table.horizontalHeader().setStretchLastSection(True)
table.horizontalHeader().hide()
table.setShowGrid(False)
box.layout().addWidget(table)
def __init__(self):
super().__init__()
self.dataset = None
self.z_values = []
self._root = None
self._displayed_root = None
self._item = None
self._cache = {}
self.colors = colorpalette.ColorPaletteGenerator(10)
box = gui.widgetBox(self.controlArea, "Axes")
self.x_var_model = itemmodels.VariableListModel()
self.comboBoxAttributesX = gui.comboBox(box,
self,
value='x_var_index',
callback=self.replot,
contentsLength=12)
self.comboBoxAttributesX.setModel(self.x_var_model)
self.y_var_model = itemmodels.VariableListModel()
self.comboBoxAttributesY = gui.comboBox(box,
self,
value='y_var_index',
callback=self.replot,
contentsLength=12)
self.comboBoxAttributesY.setModel(self.y_var_model)
box = gui.widgetBox(self.controlArea, "Color")
self.z_var_model = itemmodels.VariableListModel()
self.comboBoxClassvars = gui.comboBox(box,
self,
value='z_var_index',
callback=self._on_z_var_changed,
contentsLength=12)
self.comboBoxClassvars.setModel(self.z_var_model)
self.z_values_view = gui.listBox(
box,
self,
"selected_z_values",
"z_values",
callback=self._on_z_values_selection_changed,
selectionMode=QtGui.QListView.MultiSelection,
addSpace=False)
gui.comboBox(box,
self,
"color_scale",
label="Scale: ",
orientation="horizontal",
items=["Linear", "Square root", "Logarithmic"],
callback=self._on_color_scale_changed)
self.sampling_box = gui.widgetBox(self.controlArea, "Sampling")
sampling_options = (self.sample_times_captions +
self.sample_percentages_captions)
self.sample_combo = gui.comboBox(self.sampling_box,
self,
'sample_level',
items=sampling_options,
callback=self.update_sample)
gui.button(self.sampling_box, self, "Sharpen", self.sharpen)
gui.rubber(self.controlArea)
self.plot = pg.PlotWidget(background="w")
self.plot.setMenuEnabled(False)
self.plot.setFrameStyle(QtGui.QFrame.StyledPanel)
self.plot.setMinimumSize(500, 500)
def font_resize(font, factor, minsize=None, maxsize=None):
font = QtGui.QFont(font)
fontinfo = QtGui.QFontInfo(font)
size = fontinfo.pointSizeF() * factor
if minsize is not None:
size = max(size, minsize)
if maxsize is not None:
size = min(size, maxsize)
font.setPointSizeF(size)
return font
axisfont = font_resize(self.font(), 0.8, minsize=11)
axispen = QtGui.QPen(self.palette().color(QtGui.QPalette.Text))
axis = self.plot.getAxis("bottom")
axis.setTickFont(axisfont)
axis.setPen(axispen)
axis = self.plot.getAxis("left")
axis.setTickFont(axisfont)
axis.setPen(axispen)
self.plot.getViewBox().sigTransformChanged.connect(
self._on_transform_changed)
self.mainArea.layout().addWidget(self.plot)
def __init__(self):
super().__init__()
gui.label(self.controlArea, self, "from pandas:")
self.setSizePolicy(QSizePolicy.Maximum, QSizePolicy.Maximum)
self.allSQLSelectWidgets.append(self) # set default settings
self.domain = None
self.recentConnections = list()
self.recentConnections.append("(none)")
self.queryFile = None
self.query = ''
self.lastQuery = None
if self.lastQuery is not None:
self.query = self.lastQuery
sources = pyodbc.dataSources()
dsns = list(sources.keys())
dsns.sort()
for dsn in dsns:
self.recentConnections.append("DSN={dsn}".format(dsn=dsn))
self.connectString = self.recentConnections[0]
self.connectBox = gui.widgetBox(self.controlArea, "Database")
self.connectLineEdit = gui.lineEdit(self.connectBox,
self,
'connectString',
callback=None)
self.connectCombo = gui.comboBox(self.connectBox,
self,
'connectString',
items=self.recentConnections,
valueType=str,
sendSelectedValue=True)
self.button = gui.button(self.connectBox,
self,
'connect',
callback=self.connectDB,
disabled=0)
# query
self.splitCanvas = QSplitter(QtCore.Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitCanvas)
self.textBox = gui.widgetBox(self, 'HiveQL')
self.splitCanvas.addWidget(self.textBox)
self.queryTextEdit = QPlainTextEdit(self.query, self)
self.textBox.layout().addWidget(self.queryTextEdit)
self.selectBox = gui.widgetBox(self.controlArea, "Select statement")
# self.selectSubmitBox = QHGroupBox("", self.selectBox)
# self.queryTextEdit.setSizePolicy(QSizePolicy(QSizePolicy.Preferred, QSizePolicy.Preferred))
# self.queryTextEdit.setMinimumWidth(300)
# self.connect(self.queryTextEdit, SIGNAL('returnPressed()'), self.executeQuery)
gui.button(self.selectBox, self, "Open...", callback=self.openScript)
gui.button(self.selectBox, self, "Save...", callback=self.saveScript)
self.selectBox.setSizePolicy(
QSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding))
gui.button(self.selectBox,
self,
'format SQL!',
callback=self.format_sql,
disabled=0)
gui.button(self.selectBox,
self,
'execute!',
callback=self.executeQuery,
disabled=0)
self.domainBox = gui.widgetBox(self.controlArea, "Domain")
self.domainLabel = gui.label(self.domainBox, self, '')
# info
self.infoBox = gui.widgetBox(self.controlArea, "Info")
self.info = []
self.info.append(gui.label(self.infoBox, self, 'No data loaded.'))
self.info.append(gui.label(self.infoBox, self, ''))
self.resize(300, 300)
self.cnxn = None
def __init__(self):
super().__init__()
self.rf_model = None
self.forest = None
self.instances = None
self.clf_dataset = None
self.color_palette = None
# CONTROL AREA
# Tree info area
box_info = gui.widgetBox(self.controlArea, 'Forest')
self.ui_info = gui.widgetLabel(box_info)
# Display controls area
box_display = gui.widgetBox(self.controlArea, 'Display')
self.ui_depth_slider = gui.hSlider(
box_display, self, 'depth_limit', label='Depth', ticks=False,
) # type: QSlider
self.ui_target_class_combo = gui.comboBox(
box_display, self, 'target_class_index', label='Target class',
orientation=Qt.Horizontal, items=[], contentsLength=8,
) # type: gui.OrangeComboBox
self.ui_size_calc_combo = gui.comboBox(
box_display, self, 'size_calc_idx', label='Size',
orientation=Qt.Horizontal,
items=list(zip(*self.SIZE_CALCULATION))[0], contentsLength=8,
) # type: gui.OrangeComboBox
self.ui_zoom_slider = gui.hSlider(
box_display, self, 'zoom', label='Zoom', ticks=False, minValue=100,
maxValue=400, createLabel=False, intOnly=False,
) # type: QSlider
# Stretch to fit the rest of the unsused area
gui.rubber(self.controlArea)
self.controlArea.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Expanding)
# MAIN AREA
self.forest_model = PythagoreanForestModel(parent=self)
self.forest_model.update_item_size(self.zoom)
self.ui_depth_slider.valueChanged.connect(
self.forest_model.update_depth)
self.ui_target_class_combo.currentIndexChanged.connect(
self.forest_model.update_target_class)
self.ui_zoom_slider.valueChanged.connect(
self.forest_model.update_item_size)
self.ui_size_calc_combo.currentIndexChanged.connect(
self.forest_model.update_size_calc)
self.list_delegate = PythagorasTreeDelegate(parent=self)
self.list_view = ClickToClearSelectionListView(parent=self)
self.list_view.setWrapping(True)
self.list_view.setFlow(QListView.LeftToRight)
self.list_view.setResizeMode(QListView.Adjust)
self.list_view.setModel(self.forest_model)
self.list_view.setItemDelegate(self.list_delegate)
self.list_view.setSpacing(2)
self.list_view.setSelectionMode(QListView.SingleSelection)
self.list_view.selectionModel().selectionChanged.connect(self.commit)
self.list_view.setUniformItemSizes(True)
self.mainArea.layout().addWidget(self.list_view)
self.resize(800, 500)
# Clear to set sensible default values
self.clear()
def _create_layout(self):
self._new_webview()
box = gui.widgetBox(self.controlArea, 'Info')
self.topic_info = gui.label(box, self,
'%(n_topic_words)d words in a topic')
gui.label(box, self, '%(documents_info_str)s')
box = gui.widgetBox(self.controlArea, 'Cloud preferences')
gui.checkBox(box,
self,
'words_color',
'Color words',
callback=self.on_cloud_pref_change)
TILT_VALUES = ('no', '30°', '45°', '60°')
gui.valueSlider(box,
self,
'words_tilt',
label='Words tilt:',
values=list(range(len(TILT_VALUES))),
callback=self.on_cloud_pref_change,
labelFormat=lambda x: TILT_VALUES[x])
gui.button(box,
None,
'Regenerate word cloud',
callback=self.on_cloud_pref_change)
box = gui.widgetBox(self.controlArea, 'Words && weights')
class TableView(gui.TableView):
def __init__(self, parent):
super().__init__(parent)
self._parent = parent
self.__nope = False
def setModel(self, model):
"""Otherwise QTableView.setModel() calls
QAbstractItemView.setSelectionModel() which resets selection,
calling selectionChanged() and overwriting any selected_words
setting that may have been saved."""
self.__nope = True
super().setModel(model)
self.__nope = False
def selectionChanged(self, selected, deselected):
nonlocal model, proxymodel
super().selectionChanged(selected, deselected)
if not self.__nope:
words = {
model[proxymodel.mapToSource(index).row()][1]
for index in self.selectionModel().selectedIndexes()
}
self._parent.update_selection(words, self)
def update_selection(self, words):
nonlocal model, proxymodel
selection = QItemSelection()
for i, (_, word) in enumerate(model):
if word in words:
index = proxymodel.mapFromSource(model.index(i, 1))
selection.select(index, index)
self.__nope = True
self.clearSelection()
self.selectionModel().select(
selection,
QItemSelectionModel.Select | QItemSelectionModel.Rows)
self.__nope = False
view = self.tableview = TableView(self)
model = self.tablemodel = PyTableModel(parent=self)
proxymodel = QSortFilterProxyModel(
self,
dynamicSortFilter=True,
sortCaseSensitivity=Qt.CaseInsensitive,
sortRole=Qt.EditRole)
proxymodel.setSourceModel(model)
model.setHorizontalHeaderLabels(['Weight', 'Word'])
view.setModel(proxymodel)
box.layout().addWidget(view)
def __init__(self):
super().__init__()
# sets self.curvePoints, self.steps equidistant points from
# 1/self.steps to 1
self.updateCurvePoints()
self.scoring = [("Classification Accuracy",
Orange.evaluation.scoring.CA),
("AUC", Orange.evaluation.scoring.AUC),
("Precision", Orange.evaluation.scoring.Precision),
("Recall", Orange.evaluation.scoring.Recall)]
#: input data on which to construct the learning curve
self.data = None
#: optional test data
self.testdata = None
#: A {input_id: Learner} mapping of current learners from input channel
self.learners = OrderedDict()
#: A {input_id: List[Results]} mapping of input id to evaluation
#: results list, one for each curve point
self.results = OrderedDict()
#: A {input_id: List[float]} mapping of input id to learning curve
#: point scores
self.curves = OrderedDict()
# [start-snippet-3]
#: The current evaluating task (if any)
self._task = None # type: Optional[Task]
#: An executor we use to submit learner evaluations into a thread pool
self._executor = ThreadExecutor()
# [end-snippet-3]
# GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infoa = gui.widgetLabel(box, 'No data on input.')
self.infob = gui.widgetLabel(box, 'No learners.')
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, "Evaluation Scores")
gui.comboBox(box,
self,
"scoringF",
items=[x[0] for x in self.scoring],
callback=self._invalidate_curves)
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, "Options")
gui.spin(box,
self,
'folds',
2,
100,
step=1,
label='Cross validation folds: ',
keyboardTracking=False,
callback=lambda: self._invalidate_results()
if self.commitOnChange else None)
gui.spin(box,
self,
'steps',
2,
100,
step=1,
label='Learning curve points: ',
keyboardTracking=False,
callback=[
self.updateCurvePoints,
lambda: self._invalidate_results()
if self.commitOnChange else None
])
gui.checkBox(box, self, 'commitOnChange',
'Apply setting on any change')
self.commitBtn = gui.button(box,
self,
"Apply Setting",
callback=self._invalidate_results,
disabled=True)
gui.rubber(self.controlArea)
# table widget
self.table = gui.table(self.mainArea,
selectionMode=QTableWidget.NoSelection)
def __init__(self):
super().__init__()
self.results = None
self.scores = None
self.classifier_names = []
self.colors = []
self.line = None
self._last_score_value = -1
box = gui.vBox(self.controlArea, box="Settings")
self.target_cb = gui.comboBox(
box, self, "target_index", label="Target:",
orientation=Qt.Horizontal, callback=self.target_index_changed,
contentsLength=8, searchable=True)
gui.checkBox(
box, self, "display_rug", "Show rug",
callback=self._on_display_rug_changed)
gui.checkBox(
box, self, "fold_curves", "Curves for individual folds",
callback=self._replot)
self.classifiers_list_box = gui.listBox(
self.controlArea, self, "selected_classifiers", "classifier_names",
box="Classifier", selectionMode=QListWidget.ExtendedSelection,
sizePolicy=(QSizePolicy.Preferred, QSizePolicy.Preferred),
sizeHint=QSize(150, 40),
callback=self._on_selection_changed)
box = gui.vBox(self.controlArea, "Metrics")
combo = gui.comboBox(
box, self, "score", items=(metric.name for metric in Metrics),
callback=self.score_changed)
self.explanation = gui.widgetLabel(
box, wordWrap=True, fixedWidth=combo.sizeHint().width())
self.explanation.setContentsMargins(8, 8, 0, 0)
font = self.explanation.font()
font.setPointSizeF(0.85 * font.pointSizeF())
self.explanation.setFont(font)
gui.radioButtons(
box, self, value="output_calibration",
btnLabels=("Sigmoid calibration", "Isotonic calibration"),
label="Output model calibration", callback=self.apply)
self.info_box = gui.widgetBox(self.controlArea, "Info")
self.info_label = gui.widgetLabel(self.info_box)
gui.auto_apply(self.controlArea, self, "auto_commit", commit=self.apply)
self.plotview = pg.GraphicsView(background="w")
self.plot = pg.PlotItem(enableMenu=False)
self.plot.setMouseEnabled(False, False)
self.plot.hideButtons()
for axis_name in ("bottom", "left"):
axis = self.plot.getAxis(axis_name)
axis.setPen(pg.mkPen(color=0.0))
# Remove the condition (that is, allow setting this for bottom
# axis) when pyqtgraph is fixed
# Issue: https://github.com/pyqtgraph/pyqtgraph/issues/930
# Pull request: https://github.com/pyqtgraph/pyqtgraph/pull/932
if axis_name != "bottom": # remove if when pyqtgraph is fixed
axis.setStyle(stopAxisAtTick=(True, True))
self.plot.setRange(xRange=(0.0, 1.0), yRange=(0.0, 1.0), padding=0.05)
self.plotview.setCentralItem(self.plot)
self.mainArea.layout().addWidget(self.plotview)
self._set_explanation()
def __init__(self, parent=None, signalManager=None, stored_settings=None):
super(OWSql, self).__init__(parent=parent,
signalManager=signalManager,
stored_settings=stored_settings)
self._connection = None
vbox = gui.widgetBox(self.controlArea, "Server", addSpace=True)
box = gui.widgetBox(vbox)
self.servertext = QtGui.QLineEdit(box)
self.servertext.setPlaceholderText('Server')
if self.host:
self.servertext.setText(self.host if not self.port else '{}:{}'.
format(self.host, self.port))
box.layout().addWidget(self.servertext)
self.databasetext = QtGui.QLineEdit(box)
self.databasetext.setPlaceholderText('Database')
if self.database:
self.databasetext.setText(self.database)
box.layout().addWidget(self.databasetext)
self.usernametext = QtGui.QLineEdit(box)
self.usernametext.setPlaceholderText('Username')
if self.username:
self.usernametext.setText(self.username)
box.layout().addWidget(self.usernametext)
self.passwordtext = QtGui.QLineEdit(box)
self.passwordtext.setPlaceholderText('Password')
self.passwordtext.setEchoMode(QtGui.QLineEdit.Password)
if self.password:
self.passwordtext.setText(self.password)
box.layout().addWidget(self.passwordtext)
tables = gui.widgetBox(box, orientation='horizontal')
self.tablecombo = QtGui.QComboBox(tables)
tables.layout().addWidget(self.tablecombo)
self.tablecombo.activated[int].connect(self.select_table)
self.connectbutton = gui.button(tables,
self,
'↻',
callback=self.connect)
self.connectbutton.setSizePolicy(QtGui.QSizePolicy.Fixed,
QtGui.QSizePolicy.Fixed)
tables.layout().addWidget(self.connectbutton)
self.custom_sql = gui.widgetBox(box, orientation='vertical')
self.custom_sql.setVisible(False)
self.sqltext = QtGui.QTextEdit(self.custom_sql)
self.sqltext.setPlainText(self.sql)
self.custom_sql.layout().addWidget(self.sqltext)
self.executebtn = gui.button(self.custom_sql,
self,
'Execute',
callback=self.open_table)
box.layout().addWidget(self.custom_sql)
gui.checkBox(box,
self,
"guess_values",
"Auto-discover discrete variables.",
callback=self.open_table)
self.connect()
if self.table:
self.open_table()
def __init__(self, parent=None):
super().__init__(parent)
#: input data
self.data = None
#: Current variable discretization state
self.var_state = {}
#: Saved variable discretization settings (context setting)
self.saved_var_states = {}
self.method = 0
self.k = 5
box = gui.widgetBox(
self.controlArea, self.tr("Default Discretization"))
self.default_bbox = rbox = gui.radioButtons(
box, self, "default_method", callback=self._default_disc_changed)
options = [
self.tr("Default"),
self.tr("Leave continuous"),
self.tr("Entropy-MDL discretization"),
self.tr("Equal-frequency discretization"),
self.tr("Equal-width discretization"),
self.tr("Remove continuous attributes")
]
for opt in options[1:5]:
gui.appendRadioButton(rbox, opt)
gui.hSlider(gui.indentedBox(rbox),
self, "default_k", minValue=2, maxValue=10,
label="Num. of intervals:",
callback=self._default_disc_changed)
gui.appendRadioButton(rbox, options[-1])
vlayout = QHBoxLayout()
box = gui.widgetBox(
self.controlArea, "Individual Attribute Settings",
orientation=vlayout, spacing=8
)
# List view with all attributes
self.varview = QListView(
selectionMode=QListView.ExtendedSelection
)
self.varview.setItemDelegate(DiscDelegate())
self.varmodel = itemmodels.VariableListModel()
self.varview.setModel(self.varmodel)
self.varview.selectionModel().selectionChanged.connect(
self._var_selection_changed
)
vlayout.addWidget(self.varview)
# Controls for individual attr settings
self.bbox = controlbox = gui.radioButtons(
box, self, "method", callback=self._disc_method_changed
)
vlayout.addWidget(controlbox)
for opt in options[:5]:
gui.appendRadioButton(controlbox, opt)
gui.hSlider(gui.indentedBox(controlbox),
self, "k", minValue=2, maxValue=10,
label="Num. of intervals:",
callback=self._disc_method_changed)
gui.appendRadioButton(controlbox, options[-1])
gui.rubber(controlbox)
controlbox.setEnabled(False)
self.controlbox = controlbox
bbox = QDialogButtonBox(QDialogButtonBox.Apply)
self.controlArea.layout().addWidget(bbox)
bbox.accepted.connect(self.commit)
button = bbox.button(QDialogButtonBox.Apply)
button.clicked.connect(self.commit)
def __init__(self):
super().__init__()
self.data = None
self.n_inliers = self.n_outliers = None
box = gui.widgetBox(self.controlArea, "Information")
self.data_info_label = gui.widgetLabel(box, self.data_info_default)
self.in_out_info_label = gui.widgetLabel(box, self.in_out_info_default)
box = gui.widgetBox(self.controlArea, "Outlier detection method")
detection = gui.radioButtons(box, self, "outlier_method")
gui.appendRadioButton(detection,
"One class SVM with non-linear kernel (RBF):")
ibox = gui.indentedBox(detection)
tooltip = "An upper bound on the fraction of training errors and a " \
"lower bound of the fraction of support vectors"
gui.widgetLabel(ibox, 'Nu:', tooltip=tooltip)
self.nu_slider = gui.hSlider(ibox,
self,
"nu",
minValue=1,
maxValue=100,
ticks=10,
labelFormat="%d %%",
callback=self.nu_changed,
tooltip=tooltip)
self.gamma_spin = gui.spin(ibox,
self,
"gamma",
label="Kernel coefficient:",
step=1e-2,
spinType=float,
minv=0.01,
maxv=10,
callback=self.gamma_changed)
gui.separator(detection, 12)
self.rb_cov = gui.appendRadioButton(detection, "Covariance estimator:")
ibox = gui.indentedBox(detection)
self.l_cov = gui.widgetLabel(ibox, 'Contamination:')
self.cont_slider = gui.hSlider(ibox,
self,
"cont",
minValue=0,
maxValue=100,
ticks=10,
labelFormat="%d %%",
callback=self.cont_changed)
ebox = gui.widgetBox(ibox, box=None, orientation='horizontal')
self.cb_emp_cov = gui.checkBox(ebox,
self,
"empirical_covariance",
"Support fraction:",
callback=self.empirical_changed)
self.support_fraction_spin = gui.spin(
ebox,
self,
"support_fraction",
step=1e-1,
spinType=float,
minv=0.1,
maxv=10,
callback=self.support_fraction_changed)
gui.separator(detection, 12)
gui.button(self.controlArea,
self,
"Detect Outliers",
callback=self.commit)
self.layout().setSizeConstraint(QtGui.QLayout.SetFixedSize)
def __init__(self):
super().__init__()
# Instance variables
self.forest_type = self.CLASSIFICATION
self.model = None
self.forest_adapter = None
self.dataset = None
self.clf_dataset = None
# We need to store refernces to the trees and grid items
self.grid_items, self.ptrees = [], []
self.color_palette = None
# Different methods to calculate the size of squares
self.SIZE_CALCULATION = [
('Normal', lambda x: x),
('Square root', lambda x: sqrt(x)),
('Logarithmic', lambda x: log(x * self.size_log_scale)),
]
self.REGRESSION_COLOR_CALC = [
('None', lambda _, __: QColor(255, 255, 255)),
('Class mean', self._color_class_mean),
('Standard deviation', self._color_stddev),
]
# CONTROL AREA
# Tree info area
box_info = gui.widgetBox(self.controlArea, 'Forest')
self.ui_info = gui.widgetLabel(box_info, label='')
# Display controls area
box_display = gui.widgetBox(self.controlArea, 'Display')
self.ui_depth_slider = gui.hSlider(box_display,
self,
'depth_limit',
label='Depth',
ticks=False,
callback=self.max_depth_changed)
self.ui_target_class_combo = gui.comboBox(
box_display,
self,
'target_class_index',
label='Target class',
orientation=Qt.Horizontal,
items=[],
contentsLength=8,
callback=self.target_colors_changed)
self.ui_size_calc_combo = gui.comboBox(
box_display,
self,
'size_calc_idx',
label='Size',
orientation=Qt.Horizontal,
items=list(zip(*self.SIZE_CALCULATION))[0],
contentsLength=8,
callback=self.size_calc_changed)
self.ui_zoom_slider = gui.hSlider(box_display,
self,
'zoom',
label='Zoom',
ticks=False,
minValue=20,
maxValue=150,
callback=self.zoom_changed,
createLabel=False)
# Stretch to fit the rest of the unsused area
gui.rubber(self.controlArea)
self.controlArea.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Expanding)
# MAIN AREA
self.scene = QGraphicsScene(self)
self.scene.selectionChanged.connect(self.commit)
self.grid = OWGrid()
self.grid.geometryChanged.connect(self._update_scene_rect)
self.scene.addItem(self.grid)
self.view = QGraphicsView(self.scene)
self.view.setRenderHint(QPainter.Antialiasing, True)
self.view.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOn)
self.mainArea.layout().addWidget(self.view)
self.resize(800, 500)
self.clear()
def __init__(self, parent=None):
super().__init__(self, parent)
self.clusterDataset = None
self.referenceDataset = None
self.ontology = None
self.annotations = None
self.loadedAnnotationCode = "---"
self.treeStructRootKey = None
self.probFunctions = [stats.Binomial(), stats.Hypergeometric()]
self.selectedTerms = []
self.selectionChanging = 0
self.__state = OWGOEnrichmentAnalysis.Initializing
self.annotationCodes = []
#############
## GUI
#############
self.tabs = gui.tabWidget(self.controlArea)
## Input tab
self.inputTab = gui.createTabPage(self.tabs, "Input")
box = gui.widgetBox(self.inputTab, "Info")
self.infoLabel = gui.widgetLabel(box, "No data on input\n")
gui.button(
box,
self,
"Ontology/Annotation Info",
callback=self.ShowInfo,
tooltip="Show information on loaded ontology and annotations")
box = gui.widgetBox(self.inputTab, "Organism")
self.annotationComboBox = gui.comboBox(box,
self,
"annotationIndex",
items=self.annotationCodes,
callback=self._updateEnrichment,
tooltip="Select organism")
genebox = gui.widgetBox(self.inputTab, "Gene Names")
self.geneAttrIndexCombo = gui.comboBox(
genebox,
self,
"geneAttrIndex",
callback=self._updateEnrichment,
tooltip="Use this attribute to extract gene names from input data")
self.geneAttrIndexCombo.setDisabled(self.useAttrNames)
cb = gui.checkBox(genebox,
self,
"useAttrNames",
"Use column names",
tooltip="Use column names for gene names",
callback=self._updateEnrichment)
cb.toggled[bool].connect(self.geneAttrIndexCombo.setDisabled)
gui.button(genebox,
self,
"Gene matcher settings",
callback=self.UpdateGeneMatcher,
tooltip="Open gene matching settings dialog")
self.referenceRadioBox = gui.radioButtonsInBox(
self.inputTab,
self,
"useReferenceDataset", ["Entire genome", "Reference set (input)"],
tooltips=[
"Use entire genome for reference",
"Use genes from Referece Examples input signal as reference"
],
box="Reference",
callback=self._updateEnrichment)
self.referenceRadioBox.buttons[1].setDisabled(True)
gui.radioButtonsInBox(
self.inputTab,
self,
"aspectIndex",
["Biological process", "Cellular component", "Molecular function"],
box="Aspect",
callback=self._updateEnrichment)
## Filter tab
self.filterTab = gui.createTabPage(self.tabs, "Filter")
box = gui.widgetBox(self.filterTab, "Filter GO Term Nodes")
gui.checkBox(
box,
self,
"filterByNumOfInstances",
"Genes",
callback=self.FilterAndDisplayGraph,
tooltip="Filter by number of input genes mapped to a term")
ibox = gui.indentedBox(box)
gui.spin(ibox,
self,
'minNumOfInstances',
1,
100,
step=1,
label='#:',
labelWidth=15,
callback=self.FilterAndDisplayGraph,
callbackOnReturn=True,
tooltip="Min. number of input genes mapped to a term")
gui.checkBox(box,
self,
"filterByPValue_nofdr",
"p-value",
callback=self.FilterAndDisplayGraph,
tooltip="Filter by term p-value")
gui.doubleSpin(gui.indentedBox(box),
self,
'maxPValue_nofdr',
1e-8,
1,
step=1e-8,
label='p:',
labelWidth=15,
callback=self.FilterAndDisplayGraph,
callbackOnReturn=True,
tooltip="Max term p-value")
#use filterByPValue for FDR, as it was the default in prior versions
gui.checkBox(box,
self,
"filterByPValue",
"FDR",
callback=self.FilterAndDisplayGraph,
tooltip="Filter by term FDR")
gui.doubleSpin(gui.indentedBox(box),
self,
'maxPValue',
1e-8,
1,
step=1e-8,
label='p:',
labelWidth=15,
callback=self.FilterAndDisplayGraph,
callbackOnReturn=True,
tooltip="Max term p-value")
box = gui.widgetBox(box, "Significance test")
gui.radioButtonsInBox(box,
self,
"probFunc", ["Binomial", "Hypergeometric"],
tooltips=[
"Use binomial distribution test",
"Use hypergeometric distribution test"
],
callback=self._updateEnrichment)
box = gui.widgetBox(self.filterTab,
"Evidence codes in annotation",
addSpace=True)
self.evidenceCheckBoxDict = {}
for etype in go.evidenceTypesOrdered:
ecb = QCheckBox(etype,
toolTip=go.evidenceTypes[etype],
checked=self.useEvidenceType[etype])
ecb.toggled.connect(self.__on_evidenceChanged)
box.layout().addWidget(ecb)
self.evidenceCheckBoxDict[etype] = ecb
## Select tab
self.selectTab = gui.createTabPage(self.tabs, "Select")
box = gui.radioButtonsInBox(self.selectTab,
self,
"selectionDirectAnnotation",
["Directly or Indirectly", "Directly"],
box="Annotated genes",
callback=self.ExampleSelection)
box = gui.widgetBox(self.selectTab, "Output", addSpace=True)
gui.radioButtonsInBox(
box,
self,
"selectionDisjoint",
btnLabels=[
"All selected genes", "Term-specific genes",
"Common term genes"
],
tooltips=[
"Outputs genes annotated to all selected GO terms",
"Outputs genes that appear in only one of selected GO terms",
"Outputs genes common to all selected GO terms"
],
callback=[self.ExampleSelection, self.UpdateAddClassButton])
self.addClassCB = gui.checkBox(box,
self,
"selectionAddTermAsClass",
"Add GO Term as class",
callback=self.ExampleSelection)
# ListView for DAG, and table for significant GOIDs
self.DAGcolumns = [
'GO term', 'Cluster', 'Reference', 'p-value', 'FDR', 'Genes',
'Enrichment'
]
self.splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitter)
# list view
self.listView = GOTreeWidget(self.splitter)
self.listView.setSelectionMode(QTreeView.ExtendedSelection)
self.listView.setAllColumnsShowFocus(1)
self.listView.setColumnCount(len(self.DAGcolumns))
self.listView.setHeaderLabels(self.DAGcolumns)
self.listView.header().setSectionsClickable(True)
self.listView.header().setSortIndicatorShown(True)
self.listView.setSortingEnabled(True)
self.listView.setItemDelegateForColumn(
6, EnrichmentColumnItemDelegate(self))
self.listView.setRootIsDecorated(True)
self.listView.itemSelectionChanged.connect(self.ViewSelectionChanged)
# table of significant GO terms
self.sigTerms = QTreeWidget(self.splitter)
self.sigTerms.setColumnCount(len(self.DAGcolumns))
self.sigTerms.setHeaderLabels(self.DAGcolumns)
self.sigTerms.setSortingEnabled(True)
self.sigTerms.setSelectionMode(QTreeView.ExtendedSelection)
self.sigTerms.setItemDelegateForColumn(
6, EnrichmentColumnItemDelegate(self))
self.sigTerms.itemSelectionChanged.connect(self.TableSelectionChanged)
self.sigTableTermsSorted = []
self.graph = {}
self.inputTab.layout().addStretch(1)
self.filterTab.layout().addStretch(1)
self.selectTab.layout().addStretch(1)
self.setBlocking(True)
self._executor = ThreadExecutor()
self._init = EnsureDownloaded([(taxonomy.Taxonomy.DOMAIN,
taxonomy.Taxonomy.FILENAME),
("GO", "taxonomy.pickle")])
self._init.finished.connect(self.__initialize_finish)
self._executor.submit(self._init)
def __init__(self):
super().__init__()
box0 = gui.widgetBox(self.controlArea, " ",orientation="horizontal")
#widget buttons: compute, set defaults, help
gui.button(box0, self, "Compute", callback=self.compute)
gui.button(box0, self, "Defaults", callback=self.defaults)
gui.button(box0, self, "Help", callback=self.help1)
self.process_showers()
box = gui.widgetBox(self.controlArea, " ",orientation="vertical")
idx = -1
#widget index 0
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "ELECTRONENERGY",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 1
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "ELECTRONENERGYSPREAD",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 2
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "ELECTRONCURRENT",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 3
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "ELECTRONBEAMSIZEH",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 4
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "ELECTRONBEAMSIZEV",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 5
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "ELECTRONBEAMDIVERGENCEH",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 6
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "ELECTRONBEAMDIVERGENCEV",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 7
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "PERIODID",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 8
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "NPERIODS",
label=self.unitLabels()[idx], addSpace=True,
valueType=int, validator=QIntValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 9
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "KV",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 10
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "DISTANCE",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 11
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "GAPH",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 12
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "GAPV",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 13
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "PHOTONENERGYMIN",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 14
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "PHOTONENERGYMAX",
label=self.unitLabels()[idx], addSpace=True,
valueType=float, validator=QDoubleValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 15
idx += 1
box1 = gui.widgetBox(box)
gui.lineEdit(box1, self, "PHOTONENERGYPOINTS",
label=self.unitLabels()[idx], addSpace=True,
valueType=int, validator=QIntValidator())
self.show_at(self.unitFlags()[idx], box1)
#widget index 16
idx += 1
box1 = gui.widgetBox(box)
gui.comboBox(box1, self, "METHOD",
label=self.unitLabels()[idx], addSpace=True,
items=['US', 'URGENT', 'SRW'],
valueType=int, orientation="horizontal")
self.show_at(self.unitFlags()[idx], box1)
gui.rubber(self.controlArea)
def __init__(self):
super().__init__()
self.data = None
self._pca = None
self._transformed = None
self._variance_ratio = None
self._cumulative = None
self._init_projector()
# Components Selection
form = QFormLayout()
box = gui.widgetBox(self.controlArea,
"Components Selection",
orientation=form)
self.components_spin = gui.spin(
box,
self,
"ncomponents",
1,
MAX_COMPONENTS,
callback=self._update_selection_component_spin,
keyboardTracking=False,
addToLayout=False)
self.components_spin.setSpecialValueText("All")
self.variance_spin = gui.spin(
box,
self,
"variance_covered",
1,
100,
callback=self._update_selection_variance_spin,
keyboardTracking=False,
addToLayout=False)
self.variance_spin.setSuffix("%")
form.addRow("Components:", self.components_spin)
form.addRow("Explained variance:", self.variance_spin)
# Options
self.options_box = gui.vBox(self.controlArea, "Options")
self.normalize_box = gui.checkBox(self.options_box,
self,
"normalize",
"Normalize variables",
callback=self._update_normalize,
attribute=Qt.WA_LayoutUsesWidgetRect)
self.maxp_spin = gui.spin(self.options_box,
self,
"maxp",
1,
MAX_COMPONENTS,
label="Show only first",
callback=self._setup_plot,
keyboardTracking=False)
gui.rubber(self.controlArea)
gui.auto_apply(self.buttonsArea, self, "auto_commit")
self.plot = SliderGraph("Principal Components",
"Proportion of variance", self._on_cut_changed)
self.mainArea.layout().addWidget(self.plot)
self._update_normalize()
def add_main_layout(self):
# this is part of init, pylint: disable=attribute-defined-outside-init
form = QFormLayout()
form.setFieldGrowthPolicy(form.AllNonFixedFieldsGrow)
form.setLabelAlignment(Qt.AlignLeft)
gui.widgetBox(self.controlArea, True, orientation=form)
form.addRow(
"Neurons in hidden layers:",
gui.lineEdit(
None,
self,
"hidden_layers_input",
orientation=Qt.Horizontal,
callback=self.settings_changed,
tooltip="A list of integers defining neurons. Length of list "
"defines the number of layers. E.g. 4, 2, 2, 3.",
placeholderText="e.g. 10,"))
form.addRow(
"Activation:",
gui.comboBox(None,
self,
"activation_index",
orientation=Qt.Horizontal,
label="Activation:",
items=[i for i in self.act_lbl],
callback=self.settings_changed))
form.addRow(
"Solver:",
gui.comboBox(None,
self,
"solver_index",
orientation=Qt.Horizontal,
label="Solver:",
items=[i for i in self.solv_lbl],
callback=self.settings_changed))
self.reg_label = QLabel()
slider = gui.hSlider(None,
self,
"alpha_index",
minValue=0,
maxValue=len(self.alphas) - 1,
callback=lambda:
(self.set_alpha(), self.settings_changed()),
createLabel=False)
form.addRow(self.reg_label, slider)
self.set_alpha()
form.addRow(
"Maximal number of iterations:",
gui.spin(None,
self,
"max_iterations",
10,
1000000,
step=10,
label="Max iterations:",
orientation=Qt.Horizontal,
alignment=Qt.AlignRight,
callback=self.settings_changed))
form.addRow(
gui.checkBox(None,
self,
"replicable",
label="Replicable training",
callback=self.settings_changed,
attribute=Qt.WA_LayoutUsesWidgetRect))
