Merge pull request biolab#2699 from jerneju/spg-scaling-metas

[ENH] Scatter Plot Graph and Scaling can handle metas

Author: lanzagar

Orange/widgets/unsupervised/owmds.py

@@ -55,11 +55,6 @@ def update_data(self, attr_x, attr_y, reset_view=True):
             self.plot_widget.hideAxis(axis)
         self.plot_widget.setAspectLocked(True, 1)
 
-    def get_size_index(self):
-        if self.attr_size == "Stress":
-            return -2
-        return super().get_size_index()
-
     def compute_sizes(self):
         def scale(a):
             dmin, dmax = np.nanmin(a), np.nanmax(a)
@@ -69,17 +64,16 @@ def scale(a):
                 return np.zeros_like(a)
 
         self.master.Information.missing_size.clear()
-        size_index = self.get_size_index()
-        if size_index == -1:
+        if self.attr_size is None:
             size_data = np.full((self.n_points,), self.point_width,
                                 dtype=float)
-        elif size_index == -2:
+        elif self.attr_size == "Stress":
             size_data = scale(stress(self.master.embedding, self.master.effective_matrix))
             size_data = self.MinShapeSize + size_data * self.point_width
         else:
             size_data = \
                 self.MinShapeSize + \
-                self.scaled_data[size_index, self.valid_data] * \
+                self.scaled_data.get_column_view(self.attr_size)[0][self.valid_data] * \
                 self.point_width
         nans = np.isnan(size_data)
         if np.any(nans):
@@ -270,11 +264,6 @@ def update_regression_line(self):
 
     def init_attr_values(self):
         domain = self.data and len(self.data) and self.data.domain or None
-        if domain is not None:
-            domain = Domain(
-                attributes=domain.attributes,
-                class_vars=domain.class_vars,
-                metas=tuple(a for a in domain.metas if a.is_primitive()))
         for model in self.models:
             model.set_domain(domain)
         self.graph.attr_color = self.data.domain.class_var if domain else None
@@ -653,21 +642,12 @@ def _setup_plot(self, new=False):
         coords = np.vstack((emb_x, emb_y)).T
 
         data = self.data
-
-        primitive_metas = tuple(a for a in data.domain.metas if a.is_primitive())
-        keys = [k for k, a in enumerate(data.domain.metas) if a.is_primitive()]
-        data_metas = data.metas[:, keys].astype(float)
-
-        attributes = self.data.domain.attributes + (self.variable_x, self.variable_y) + \
-                     primitive_metas
+        attributes = data.domain.attributes + (self.variable_x, self.variable_y)
         domain = Domain(attributes=attributes,
-                        class_vars=self.data.domain.class_vars)
-        if data_metas is not None:
-            data_x = (self.data.X, coords, data_metas)
-        else:
-            data_x = (self.data.X, coords)
-        data = Table.from_numpy(domain, X=hstack(data_x),
-                                Y=self.data.Y)
+                        class_vars=data.domain.class_vars,
+                        metas=data.domain.metas)
+        data = Table.from_numpy(domain, X=hstack((data.X, coords)),
+                                Y=data.Y, metas=data.metas)
         subset_data = data[self._subset_mask] if self._subset_mask is not None else None
         self.graph.new_data(data, subset_data=subset_data, new=new)
         self.graph.update_data(self.variable_x, self.variable_y, True)

Orange/widgets/utils/scaling.py

@@ -1,5 +1,8 @@
+from itertools import chain
+
 import numpy as np
 
+from Orange.data import Domain
 from Orange.statistics.basic_stats import DomainBasicStats
 from Orange.widgets.settings import Setting
 from Orange.widgets.utils import checksum
@@ -12,12 +15,11 @@ class ScaleData:
 
     def _reset_data(self):
         self.domain = None
-        self.data = None
-        self.original_data = None  # as numpy array
+        self.data = None  # as Orange Table
         self.scaled_data = None  # in [0, 1]
         self.jittered_data = None
         self.attr_values = {}
-        self.domain_data_stat = []
+        self.domain_data_stat = {}
         self.valid_data_array = None
         self.attribute_flip_info = {}  # dictionary with attr: 0/1 if flipped
         self.jitter_seed = 0
@@ -30,53 +32,58 @@ def rescale_data(self):
 
     def _compute_domain_data_stat(self):
         stt = self.domain_data_stat = \
-            getCached(self.data, DomainBasicStats, (self.data,))
-        for index in range(len(self.domain)):
-            attr = self.domain[index]
+            getCached(self.data, DomainBasicStats, (self.data, True))
+        domain = self.domain
+        for attr in chain(domain.variables, domain.metas):
             if attr.is_discrete:
                 self.attr_values[attr] = [0, len(attr.values)]
             elif attr.is_continuous:
-                self.attr_values[attr] = [stt[index].min, stt[index].max]
+                self.attr_values[attr] = [stt[attr].min, stt[attr].max]
 
     def _compute_scaled_data(self):
         data = self.data
         # We cache scaled_data and validArray to share them between widgets
         cached = getCached(data, "visualizationData")
         if cached:
-            self.original_data, self.scaled_data, self.valid_data_array = cached
+            self.data, self.scaled_data, self.valid_data_array = cached
             return
 
         Y = data.Y if data.Y.ndim == 2 else np.atleast_2d(data.Y).T
-        self.original_data = np.hstack((data.X, Y)).T
-        self.scaled_data = no_jit = self.original_data.copy()
-        self.valid_data_array = np.isfinite(no_jit)
-        for index in range(len(data.domain)):
-            attr = data.domain[index]
+        if np.any(data.metas):
+            all_data = (data.X, Y, data.metas)
+        else:
+            all_data = (data.X, Y)
+        all_data = np.hstack(all_data).T
+        self.scaled_data = self.data.copy()
+        self.valid_data_array = np.isfinite(all_data)
+        domain = self.domain
+        for attr in chain(domain.attributes, domain.class_vars, domain.metas):
+            c = self.scaled_data.get_column_view(attr)[0]
             if attr.is_discrete:
-                no_jit[index] *= 2
-                no_jit[index] += 1
-                no_jit[index] /= 2 * len(attr.values)
+                c += 0.5
+                c /= len(attr.values)
             else:
-                dstat = self.domain_data_stat[index]
-                no_jit[index] -= dstat.min
+                dstat = self.domain_data_stat[attr]
+                c -= dstat.min
                 if dstat.max != dstat.min:
-                    no_jit[index] /= dstat.max - dstat.min
+                    c /= dstat.max - dstat.min
         setCached(data, "visualizationData",
-                  (self.original_data, self.scaled_data, self.valid_data_array))
+                  (self.data, self.scaled_data, self.valid_data_array))
 
     def _compute_jittered_data(self):
         data = self.data
         self.jittered_data = self.scaled_data.copy()
         random = np.random.RandomState(seed=self.jitter_seed)
-        for index, col in enumerate(self.jittered_data):
+        domain = self.domain
+        for attr in chain(domain.variables, domain.metas):
             # Need to use a different seed for each feature
-            attr = data.domain[index]
             if attr.is_discrete:
                 off = self.jitter_size / (25 * max(1, len(attr.values)))
             elif attr.is_continuous and self.jitter_continuous:
                 off = self.jitter_size / 25
             else:
                 continue
+            col = self.jittered_data.get_column_view(attr)[0]
             col += random.uniform(-off, off, len(data))
             # fix values outside [0, 1]
             col = np.absolute(col)
@@ -92,8 +99,13 @@ def set_data(self, data, skip_if_same=False, no_data=False):
         if data is None:
             return
 
-        self.domain = data.domain
-        self.data = data
+        domain = data.domain
+        new_domain = Domain(attributes=domain.attributes,
+                            class_vars=domain.class_vars,
+                            metas=tuple(v for v in domain.metas if v.is_primitive()))
+        self.data = data.transform(new_domain)
+        self.data.metas = self.data.metas.astype(float)
+        self.domain = self.data.domain
         self.attribute_flip_info = {}
         if not no_data:
             self._compute_domain_data_stat()
@@ -103,67 +115,73 @@ def set_data(self, data, skip_if_same=False, no_data=False):
     def flip_attribute(self, attr):
         if attr.is_discrete:
             return 0
-        index = self.domain.index(attr)
         self.attribute_flip_info[attr] = 1 - self.attribute_flip_info.get(attr, 0)
         if attr.is_continuous:
             self.attr_values[attr] = [-self.attr_values[attr][1],
                                       -self.attr_values[attr][0]]
-
-        self.jittered_data[index] = 1 - self.jittered_data[index]
-        self.scaled_data[index] = 1 - self.scaled_data[index]
+        col = self.jittered_data.get_column_view(attr)[0]
+        col *= -1
+        col += 1
+        col = self.scaled_data.get_column_view(attr)[0]
+        col *= -1
+        col += 1
         return 1
 
-    def get_valid_list(self, indices):
+    def get_valid_list(self, attrs):
         """
         Get array of 0 and 1 of len = len(self.data). If there is a missing
         value at any attribute in indices return 0 for that instance.
         """
         if self.valid_data_array is None or len(self.valid_data_array) == 0:
             return np.array([], np.bool)
+        domain = self.domain
+        indices = []
+        for index, attr in enumerate(chain(domain.variables, domain.metas)):
+            if attr in attrs:
+                indices.append(index)
         return np.all(self.valid_data_array[indices], axis=0)
 
-    def get_valid_indices(self, indices):
+    def get_valid_indices(self, attrs):
         """
         Get array with numbers that represent the instance indices that have a
         valid data value.
         """
-        valid_list = self.get_valid_list(indices)
+        valid_list = self.get_valid_list(attrs)
         return np.nonzero(valid_list)[0]
 
 
 class ScaleScatterPlotData(ScaleData):
-    def get_xy_data_positions(self, xattr, yattr, filter_valid=False,
+    def get_xy_data_positions(self, attr_x, attr_y, filter_valid=False,
                               copy=True):
         """
         Create x-y projection of attributes in attrlist.
 
         """
-        xattr_index = self.domain.index(xattr)
-        yattr_index = self.domain.index(yattr)
+        jit = self.jittered_data
         if filter_valid is True:
-            filter_valid = self.get_valid_list([xattr_index, yattr_index])
+            filter_valid = self.get_valid_list([attr_x, attr_y])
         if isinstance(filter_valid, np.ndarray):
-            xdata = self.jittered_data[xattr_index, filter_valid]
-            ydata = self.jittered_data[yattr_index, filter_valid]
+            data_x = jit.get_column_view(attr_x)[0][filter_valid]
+            data_y = jit.get_column_view(attr_y)[0][filter_valid]
         elif copy:
-            xdata = self.jittered_data[xattr_index].copy()
-            ydata = self.jittered_data[yattr_index].copy()
+            data_x = jit.get_column_view(attr_x)[0].copy()
+            data_y = jit.get_column_view(attr_y)[0].copy()
         else:
-            xdata = self.jittered_data[xattr_index]
-            ydata = self.jittered_data[yattr_index]
+            data_x = jit.get_column_view(attr_x)[0]
+            data_y = jit.get_column_view(attr_y)[0]
 
-        if self.domain[xattr_index].is_discrete:
-            xdata *= len(self.domain[xattr_index].values)
-            xdata -= 0.5
+        if attr_x.is_discrete:
+            data_x *= len(attr_x.values)
+            data_x -= 0.5
         else:
-            xdata *= self.attr_values[xattr][1] - self.attr_values[xattr][0]
-            xdata += float(self.attr_values[xattr][0])
-        if self.domain[yattr_index].is_discrete:
-            ydata *= len(self.domain[yattr_index].values)
-            ydata -= 0.5
+            data_x *= self.attr_values[attr_x][1] - self.attr_values[attr_x][0]
+            data_x += float(self.attr_values[attr_x][0])
+        if attr_y.is_discrete:
+            data_y *= len(attr_y.values)
+            data_y -= 0.5
         else:
-            ydata *= self.attr_values[yattr][1] - self.attr_values[yattr][0]
-            ydata += float(self.attr_values[yattr][0])
-        return xdata, ydata
+            data_y *= self.attr_values[attr_y][1] - self.attr_values[attr_y][0]
+            data_y += float(self.attr_values[attr_y][0])
+        return data_x, data_y
 
     getXYDataPositions = get_xy_data_positions

Orange/widgets/visualize/owscatterplot.py

@@ -47,9 +47,12 @@ def iterate_states(self, initial_state):
 
     def compute_score(self, state):
         graph = self.master.graph
-        ind12 = [graph.domain.index(self.attrs[x]) for x in state]
-        valid = graph.get_valid_list(ind12)
-        X = graph.jittered_data[ind12, :][:, valid].T
+        attrs = [self.attrs[x] for x in state]
+        valid = graph.get_valid_list(attrs)
+        cols = []
+        for var in attrs:
+            cols.append(graph.jittered_data.get_column_view(var)[0][valid])
+        X = np.column_stack(cols)
         Y = self.master.data.Y[valid]
         if X.shape[0] < self.minK:
             return
@@ -66,7 +69,7 @@ def bar_length(self, score):
         return max(0, -score)
 
     def score_heuristic(self):
-        X = self.master.graph.jittered_data.T
+        X = self.master.graph.jittered_data.X
         Y = self.master.data.Y
         mdomain = self.master.data.domain
         dom = Domain([ContinuousVariable(str(i)) for i in range(X.shape[1])],
@@ -139,7 +142,6 @@ def __init__(self):
 
         self.data = None  # Orange.data.Table
         self.subset_data = None  # Orange.data.Table
-        self.data_metas_X = None  # self.data, where primitive metas are moved to X
         self.sql_data = None  # Orange.data.sql.table.SqlTable
         self.attribute_selection_list = None  # list of Orange.data.Variable
         self.__timer = QTimer(self, interval=1200)
@@ -243,7 +245,6 @@ def set_data(self, data):
         same_domain = (self.data and data and
                        data.domain.checksum() == self.data.domain.checksum())
         self.data = data
-        self.data_metas_X = self.move_primitive_metas_to_X(data)
 
         if not same_domain:
             self.init_attr_values()
@@ -295,7 +296,6 @@ def add_data(self, time=0.4):
             data_sample.download_data(2000, partial=True)
             data = Table(data_sample)
             self.data = Table.concatenate((self.data, data), axis=0)
-            self.data_metas_X = self.move_primitive_metas_to_X(self.data)
             self.handleNewSignals()
 
     def switch_sampling(self):
@@ -304,15 +304,6 @@ def switch_sampling(self):
             self.add_data()
             self.__timer.start()
 
-    def move_primitive_metas_to_X(self, data):
-        if data is not None:
-            new_attrs = [a for a in data.domain.attributes + data.domain.metas
-                         if a.is_primitive()]
-            new_metas = [m for m in data.domain.metas if not m.is_primitive()]
-            new_domain = Domain(new_attrs, data.domain.class_vars, new_metas)
-            data = data.transform(new_domain)
-        return data
-
     @Inputs.data_subset
     def set_subset_data(self, subset_data):
         self.warning()
@@ -322,12 +313,11 @@ def set_subset_data(self, subset_data):
             else:
                 self.warning("Data subset does not support large Sql tables")
                 subset_data = None
-        self.subset_data = self.move_primitive_metas_to_X(subset_data)
         self.controls.graph.alpha_value.setEnabled(subset_data is None)
 
     # called when all signals are received, so the graph is updated only once
     def handleNewSignals(self):
-        self.graph.new_data(self.data_metas_X, self.subset_data)
+        self.graph.new_data(self.data, self.subset_data)
         if self.attribute_selection_list and self.graph.domain and \
                 all(attr in self.graph.domain
                         for attr in self.attribute_selection_list):