Commits

Aleš Erjavec committed 54642c2

More work on Quality Control widget (now in semi-useful state).

Comments (0)

Files changed (1)

widgets/prototypes/OWQualityControl.py

 """
-<name>Quality control</name>
+<name>Quality Control</name>
 
 """
 
 
 from OWWidget import *
 from OWItemModels import PyListModel
+from OWGraphics import GraphicsSimpleTextLayoutItem, GtI
 import OWGUI
 
+from OWGenotypeDistances import SetContextHandler
+
 import obiExperiments as exp
 import numpy
 
+from collections import defaultdict
+from contextlib import contextmanager
 from pprint import pprint
 
-def compute_within_group_distances(data, groups, distance=exp.dist_pcorr):
-    matrices = []
-    for _, indices in groups:
-        matrix = Orange.misc.SymMatrix(len(group_i))
-        for i, index_i in enumerate(indices):
-            for j, index_j in enumerate(indics[i + 1:], i + 1):
-                vec_i = exp.linearize(data, [index_i])
-                vec_j = exp.linearize(data, [index_j])
-                matrix[i, j] = distance(vec_i, vec_j)
-        metrices.append(matrix)
-    return matrices
+DEBUG = False
 
-def group_label(splits, group):
+@contextmanager
+def control_disable(widget):
+    widget.setEnabled(False)
+    yield
+    widget.setEnabled(True)
+    
+@contextmanager
+def disable_updates(widget):
+    widget._disable_updates = True
+    yield
+    widget._disable_updates = False
+
+def group_label(splits, groups):
     """
     Return group label
     """
     return " | ".join(labels)
 
 
+def sort_label(sort, attr):
+    """
+    Return within group sorted items label for attribute.
+    """
+    items = [(key, attr.attributes.get(key, "?")) \
+             for key in sort]
+    labels = ["{}={}".format(*item) for item in items]
+    return " | ".join(labels)
+
+def float_if_posible(val):
+    try:
+        return float(val)
+    except ValueError:
+        return val
 
 class OWQualityControl(OWWidget):
+    contextHandlers = {"": SetContextHandler("")}
     settingsList = []
+    
     DISTANCE_FUNCTIONS = [("Distance from Pearson correlation", exp.dist_pcorr),
                           ("Euclidean distance", exp.dist_eucl),
                           ("Distance from Spearman correlation", exp.dist_spearman)]
 
         self.inputs = [("Experiment Data", Orange.data.Table, self.set_data)]
 
-        ## Setings
+        ## Settings
         self.selected_distance_index = 0
         self.replicate_id = "replicate"
 
         self.data = None
         self.distances = None
         self.groups = None
-        self.group_indices = None
-        self.separate_by = None
-        self.sort_by = None
+        self.unique_pos = None
+        self.base_index = 0
 
         ## GUI
         box = OWGUI.widgetBox(self.controlArea, "Info")
         box = OWGUI.widgetBox(self.controlArea, "Split By")
         self.split_by_model = PyListModel()
         self.split_by_view = QListView()
+        self.split_by_view.setSelectionMode(QListView.ExtendedSelection)
         self.split_by_view.setModel(self.split_by_model)
         box.layout().addWidget(self.split_by_view)
 
+        self.connect(self.split_by_view.selectionModel(),
+                     SIGNAL("selectionChanged(QItemSelection, QItemSelection)"),
+                     self.on_split_key_changed)
+
         ## Sort By box
         box = OWGUI.widgetBox(self.controlArea, "Sort By")
         self.sort_by_model = PyListModel()
         self.sort_by_view = QListView()
+        self.sort_by_view.setSelectionMode(QListView.ExtendedSelection)
         self.sort_by_view.setModel(self.sort_by_model)
         box.layout().addWidget(self.sort_by_view)
+        
+        self.connect(self.sort_by_view.selectionModel(),
+                     SIGNAL("selectionChanged(QItemSelection, QItemSelection)"),
+                     self.on_sort_key_changed)
 
         ## Distance box
         box = OWGUI.widgetBox(self.controlArea, "Distance Measure")
         OWGUI.comboBox(box, self, "selected_distance_index",
-                       items=[t[0] for t in self.DISTANCE_FUNCTIONS])
+                       items=[t[0] for t in self.DISTANCE_FUNCTIONS],
+                       callback=self.on_distance_measure_changed)
 
+        self.connect(self.graphButton,
+                     SIGNAL("clicked()"),
+                     self.save_graph)
+        
         self.scene = QGraphicsScene()
-        self.scene_view = QGraphicsView(self.scene)
+        self.scene_view = QualityGraphicsView(self.scene)
+        self.scene_view.setRenderHints(QPainter.Antialiasing)
         self.mainArea.layout().addWidget(self.scene_view)
+        
+        self.connect(self.scene_view,
+                     SIGNAL("view_size_changed(QSize)"),
+                     self.on_view_resize)
 
+        self._disable_updates = False
+        self.main_widget = None
+        
         self.resize(800, 600)
 
     def clear(self):
         self.data = None
         self.distances = None
         self.groups = None
-        self.group_indices = None
-        self.separate_by = None
-        self.sort_by = None
+        self.unique_pos = None
+        
+        with disable_updates(self):
+            self.split_by_model[:] = []
+            self.sort_by_model[:] = []
 
         self.scene.clear()
+        self.info_box.setText("\n")
 
     def set_data(self, data=None):
         """Set input experiment data.
         if self.data:
             self.on_new_data()
         else:
+            self.closeContext("")
             self.clear()
 
     def update_label_candidates(self):
         (Group/Sort By views).
         
         """
-        pass
+        keys = self.get_suitable_keys(self.data)
+        with disable_updates(self):
+            self.split_by_model[:] = keys
+            self.sort_by_model[:] = keys
+        
+    def get_suitable_keys(self, data):
+        """ Return suitable attr label keys from the data where the key has at least
+        two unique values in the data.
+        
+        """
+        attrs = [attr.attributes.items() for attr in data.domain.attributes]
+        attrs  = reduce(list.__add__, attrs, [])
+        # in case someone put non string values in attributes dict
+        attrs = [(str(key), str(value)) for key, value in attrs]
+        attrs = set(attrs)
+        values = defaultdict(set)
+        for key, value in attrs:
+            values[key].add(value)
+        keys = [key for key in values if len(values[key]) > 1]
+        return keys
 
     def selected_split_by_labels(self):
         """Return the current selected split labels.
         """
-        return ["tp"]
+        sel_m = self.split_by_view.selectionModel()
+        indices = [r.row() for r in sel_m.selectedRows()]
+        return [self.sort_by_model[i] for i in indices]
 
     def selected_sort_by_labels(self):
         """Return the current selected sort labels
         """
-        return ["replicate"]
+        sel_m = self.sort_by_view.selectionModel()
+        indices = [r.row() for r in sel_m.selectedRows()]
+        return [self.sort_by_model[i] for i in indices]
 
     def selected_distance(self):
         """Return the selected distance function.
         """
         return self.DISTANCE_FUNCTIONS[self.selected_distance_index][1]
+    
+    def selected_base_index(self):
+        return self.base_index
 
     def on_new_data(self):
         """We have new data and need to recompute all.
         """
+        self.closeContext("")
+        
         self.update_label_candidates()
-
-        self.separate_by = self.selected_split_by_labels()
-        self.sort_by = self.selected_sort_by_labels()
-
+        self.info_box.setText("{} genes \n{} experiments".format(
+                                len(self.data), 
+                                len(self.data.domain.attributes)
+                                )
+                              )
+        
+        keys = self.get_suitable_keys(self.data)
+        self.openContext("", keys)
+        
+        ## Restore saved context
+        context = self.currentContexts[""]
+        split_by_labels= getattr(context, "split_by_labels", set())
+        sort_by_labels = getattr(context, "sort_by_labels", set())
+        
+        def select(model, selection_model, selected_items):
+            all_items = list(model)
+            try:
+                indices = [all_items.index(item) for item in selected_items]
+            except:
+                indices = []
+            for ind in indices:
+                selection_model.select(model.index(ind), QItemSelectionModel.Select)
+                
+#        self._disable_updates = True
+#        try:
+        with disable_updates(self):
+            select(self.split_by_view.model(),
+                   self.split_by_view.selectionModel(),
+                   split_by_labels)
+            
+            select(self.sort_by_view.model(),
+                   self.sort_by_view.selectionModel(),
+                   sort_by_labels)
+#        finally:
+#            self._disable_updates = False
+            
         self.split_and_update()
-
+        
+    def on_split_key_changed(self, *args):
+        with control_disable(self):
+            if not self._disable_updates:
+                context = self.currentContexts[""]
+                context.split_by_labels = self.selected_split_by_labels()
+                self.split_and_update()
+    
+    def on_sort_key_changed(self, *args):
+        with control_disable(self):
+            if not self._disable_updates:
+                context = self.currentContexts[""]
+                context.sort_by_labels = self.selected_sort_by_labels()
+                self.split_and_update()
+        
+    def on_distance_measure_changed(self):
+        self.update_distances()
+        self.replot_experiments()
+        
+    def on_view_resize(self, size):
+        if self.main_widget:
+            current = self.main_widget.size()
+            self.main_widget.resize(size.width() - 2, 
+                                    current.height())
+            
+            self.scene.setSceneRect(self.scene.itemsBoundingRect())
+        
+    def on_rug_item_clicked(self, item):
+        base = item.index
+        if base != self.base_index:
+            self.base_index = base
+            self.split_and_update()
+        
     def split_and_update(self):
         """
         Split the data based on the selected sort/split labels
         and update the quality plot.
         
         """
-        self.groups, self.group_indices = \
-                exp.separate_by(self.data, self.separate_by,
-                                consider=self.sort_by,
-                                add_empty=False)
-
-        self.groups = sorted(self.groups.items())
-        self.group_indices = sorted(self.group_indices.items())
+        self.groups, self.unique_pos = \
+                exp.separate_by(self.data,
+                                self.selected_split_by_labels(),
+                                consider=self.selected_sort_by_labels(),
+                                add_empty=True)
+        
+        
+        self.groups = sorted(self.groups.items(),
+                             key=lambda t: map(float_if_posible, t[0]))
+        self.unique_pos = sorted(self.unique_pos.items(),
+                                 key=lambda t: map(float_if_posible, t[0]))
         
         pprint(self.groups)
-        pprint(self.group_indices)
-
-        self.update_distances()
-        self.replot_experiments()
+        pprint(self.unique_pos)
+        if self.groups:
+            # TODO: Check if the groups of base experiment have changed
+            self.update_distances()
+            self.replot_experiments()
 
     def update_distances(self):
         """Recompute the experiment distances.
         """
         distance = self.selected_distance()
-        base_index = 0
+        base_index = self.base_index
         base_distances = []
+        pb = OWGUI.ProgressBar(self, len(self.groups) * \
+                               len(self.data.domain.attributes))
         for group, indices in self.groups:
             # Base column of the group
-            base_vec = exp.linearize(self.data, [indices[base_index]])
-            distances = []
-            # Compute the distances between base replicate 
-            # and all the rest data columns.
-            for i in range(len(self.data.domain.attributes)):
-                if i == indices[base_index]:
-                    distances.append(0.0)
-                else:
-                    vec_i = exp.linearize(self.data, [i])
-                    distances.append(distance(base_vec, vec_i))
-            base_distances.append(distances)
-            
+            if indices[base_index] is not None:
+                base_vec = exp.linearize(self.data, [indices[base_index]])
+                distances = []
+                # Compute the distances between base replicate 
+                # and all the rest data columns.
+                for i in range(len(self.data.domain.attributes)):
+                    if i == indices[base_index]:
+                        distances.append(0.0)
+                    else:
+                        vec_i = exp.linearize(self.data, [i])
+                        distances.append(distance(base_vec, vec_i))
+                    pb.advance()
+                    
+                base_distances.append(distances)
+            else:
+                base_distances.append(None)
+        pb.finish()
         self.distances = base_distances
-#        distance = self.selected_distance()
-#        self.distances = \
-#            compute_within_group_distances(self.data, self.groups, distance)
-#        self.backgroud_distances = \
-#            compute_within_group_distances( \
-#                            self.data, 
-#                            [(None,  
-#                             range(len(self.data.attributes)))],
-#                            distance
-#                            )
-#        print self.distances
-#        print self.backgroud_distances
 
     def replot_experiments(self):
         """Replot the whole quality plot
         self.scene.clear()
         labels = []
         ## Base replicate=1 TODO: the index should be set
-        base_index = 0
-        max_dist = numpy.max(self.distances)
+        base_index = self.base_index
+        max_dist = numpy.max(filter(None, self.distances))
+        print max_dist
         rug_widgets = []
+        
+        group_pen = QPen(QColor(0, 0, 0))
+        group_pen.setWidth(2)
+        group_pen.setCapStyle(Qt.RoundCap)
+        background_pen = QPen(QColor(0, 0, 250, 150))
+        background_pen.setWidth(1)
+        background_pen.setCapStyle(Qt.RoundCap)
+        
+        main_widget = QualityControlWidget()
+        layout = QGraphicsGridLayout()
+        split_by = self.selected_split_by_labels()
+        sort_by = self.selected_sort_by_labels()
+        attributes = self.data.domain.attributes
         if self.data:
             for (group, indices), dist_vec in zip(self.groups, self.distances):
                 base = indices[base_index]
                 indices_set = set(indices)
                 rug_items = []
-                for i in range(len(self.data.domain.attributes)):
-                    # Is this a within group distance or background
-                    in_group = i in indices_set 
-                    rug_item = RugItem(dist_vec[i] / max_dist)
-                    rug_items.append(rug_item)
+                if dist_vec is not None:
+                    for i, attr in enumerate(attributes):
+                        # Is this a within group distance or background
+                        in_group = i in indices_set 
+                        if in_group:
+                            rug_item = ClickableRugItem(dist_vec[i] / max_dist,
+                                           1.0, self.on_rug_item_clicked)
+                            rug_item.setPen(group_pen)
+                            tooltip = sort_label(split_by, attr)
+                            tooltip += "\n" + sort_label(sort_by, attr)
+                            rug_item.setToolTip(tooltip)
+                            rug_item.setToolTip(sort_label(sort_by, attr))
+                            rug_item.index = indices.index(i)
+                        else:
+#                            rug_item = RugItem(dist_vec[i] / max_dist, 0.85)
+                            rug_item = ClickableRugItem(dist_vec[i] / max_dist,
+                                           0.85, None)#self.on_rug_item_clicked)
+                            tooltip = sort_label(split_by, attr)
+                            tooltip += "\n" + sort_label(sort_by, attr)
+                            rug_item.setToolTip(tooltip)
+                            rug_item.setPen(background_pen)
+                        rug_items.append(rug_item)
                     
                 rug_widget = RugGraphicsWidget()
                 rug_widget.set_rug(rug_items)
+                
                 rug_widgets.append(rug_widget)
                 
-        layout = QGraphicsLinearLayout(Qt.Vertical)
-        for w in rug_widgets:
-            layout.addItem(w)
+                label = group_label(self.selected_split_by_labels(), group)
+#                label_item = QGraphicsSimpleTextItem(label)
+                label_item = GtI(label, main_widget)
+                label_item = GraphicsSimpleTextLayoutItem(label_item)
+                label_item.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
+                labels.append(label_item)
+        
+        for i, (label, w) in enumerate(zip(labels, rug_widgets)):
+            layout.addItem(label, i, 0, Qt.AlignVCenter)
+            layout.addItem(w, i, 1)
+            layout.setRowMaximumHeight(i, 30)
             
-        main_widget = QGraphicsWidget()
         main_widget.setLayout(layout)
-        main_widget.resize(600, 600)
         self.scene.addItem(main_widget)
+        main_widget.show()
+        self.main_widget = main_widget
+        self.rug_widgets = rug_widgets
+        self.labels = labels
+        self.on_view_resize(self.scene_view.size())
         
-                    
+    def save_graph(self):
+        from OWDlgs import OWChooseImageSizeDlg
+        dlg = OWChooseImageSizeDlg(self.scene, parent=self)
+        dlg.exec_()
 
 
 class RugGraphicsWidget(QGraphicsWidget):
         QGraphicsWidget.__init__(self, parent)
         self.rug_items = []
         self.set_rug(rug)
-
+        self.setMaximumHeight(30)
+        self.setMinimumHeight(30)
+        
     def clear(self):
         """
         Clear all rug items from this widget and remove them 
         width = size.width()
         
         for item in self.rug_items:
+            offset = (1.0 - item.height) * height / 2.0
             item.setPos(width * item.value, 0)
-            item.setLine(0., 0., 0., height)
-            
+            item.setLine(0., offset, 0., height - offset)
 
     def resizeEvent(self, event):
         QGraphicsWidget.resizeEvent(self, event)
 
 
 class RugItem(QGraphicsLineItem):
-    def __init__(self, value):
+    def __init__(self, value, height):
         QGraphicsLineItem.__init__(self)
         self.value = value
+        self.height = height
 
     def set_height(self, height):
-        """Set the height of this item.
+        """Set the height of this item (in ratio of the rug height)
         """
         self.height = height
+        
+class ClickableRugItem(RugItem):
+    def __init__(self, value, height, on_pressed):
+        RugItem.__init__(self, value, height)
+        self.on_pressed = on_pressed
+        self.setAcceptedMouseButtons(Qt.LeftButton)
+        self.setAcceptHoverEvents(True)
+        
+    def mousePressEvent(self, event):
+        if event.button() == Qt.LeftButton and self.on_pressed:
+            self.on_pressed(self)
+            
+    def hoverEnterEvent(self, event):
+        pen = QPen(self.pen())
+        pen.setWidthF(3)
+        self.setPen(pen)
+        return RugItem.hoverEnterEvent(self, event)
+    
+    def hoverLeaveEvent(self, event):
+        pen = QPen(self.pen())
+        pen.setWidth(2)
+        self.setPen(pen)
+        return RugItem.hoverLeaveEvent(self, event)
 
 
+class QualityGraphicsView(QGraphicsView):
+    def resizeEvent(self, event):
+        QGraphicsView.resizeEvent(self, event)
+        self.emit(SIGNAL("view_size_changed(QSize)"),
+                  event.size())
 
+
+class QualityControlWidget(QGraphicsWidget):
+    if DEBUG:
+        def paint(self, painter, options, widget=0):
+            rect =  self.geometry()
+            rect.translate(-self.pos())
+            painter.drawRect(rect)
+            
 if __name__ == "__main__":
     app = QApplication(sys.argv)
     w = OWQualityControl()
-    data = Orange.data.Table("doc:dicty-abc-sample.tab")
+#    data = Orange.data.Table("doc:dicty-abc-sample.tab")
+    data = Orange.data.Table("doc:pipa.tab")
 
     w.set_data(data)
     w.show()
     w.handleNewSignals()
     app.exec_()
-
+    w.set_data(None)
+    w.handleNewSignals()
+    w.saveSettings()