Merge pull request #935 from janezd/bootstrap-sample

OWDataSampler: Add bootstrap, minor fixes in GUI

Orange/widgets/data/owdatasampler.py

@@ -29,7 +29,7 @@ class OWDataSampler(widget.OWWidget):
     resizing_enabled = False
 
     RandomSeed = 42
-    FixedProportion, FixedSize, CrossValidation = range(3)
+    FixedProportion, FixedSize, CrossValidation, Bootstrap = range(4)
     SqlTime, SqlProportion = range(2)
 
     use_seed = Setting(False)
@@ -69,7 +69,8 @@ def f():
             gui.indentedBox(sampling), self,
             "sampleSizePercentage",
             minValue=0, maxValue=99, ticks=10, labelFormat="%d %%",
-            callback=set_sampling_type(self.FixedProportion))
+            callback=set_sampling_type(self.FixedProportion),
+            addSpace=12)
 
         gui.appendRadioButton(sampling, "Fixed sample size:")
         ibox = gui.indentedBox(sampling)
@@ -79,10 +80,9 @@ def f():
             callback=set_sampling_type(self.FixedSize))
         gui.checkBox(
             ibox, self, "replacement", "Sample with replacement",
-            callback=set_sampling_type(self.FixedSize))
-        gui.separator(sampling, 12)
+            callback=set_sampling_type(self.FixedSize),
+            addSpace=12)
 
-        gui.separator(sampling, 12)
         gui.appendRadioButton(sampling, "Cross Validation:")
         form = QtGui.QFormLayout(
             formAlignment=Qt.AlignLeft | Qt.AlignTop,
@@ -99,6 +99,8 @@ def f():
             addToLayout=False, callback=self.fold_changed)
         form.addRow("Selected fold", self.selected_fold_spin)
 
+        gui.appendRadioButton(sampling, "Boostrap")
+
         self.sql_box = gui.widgetBox(self.controlArea, "Sampling Type")
         sampling = gui.radioButtons(self.sql_box, self, "sampling_type",
                                     callback=self.sampling_type_changed)
@@ -115,6 +117,7 @@ def f():
         spin.setSuffix(" %")
         self.sql_box.setVisible(False)
 
+
         self.options_box = gui.widgetBox(self.controlArea, "Options")
         self.cb_seed = gui.checkBox(
             self.options_box, self, "use_seed",
@@ -129,7 +132,8 @@ def f():
         self.cb_sql_dl.setVisible(False)
 
         gui.button(self.controlArea, self, "Sample Data",
-                   callback=self.commit)
+                   callback=self.commit, addSpace=8)
+        self.controlArea.layout().addWidget(self.report_button)
 
     def sampling_type_changed(self):
         self.settings_changed()
@@ -190,12 +194,13 @@ def commit(self):
                 self.updateindices()
                 if self.indices is None:
                     return
-            if self.sampling_type in [self.FixedProportion, self.FixedSize]:
+            if self.sampling_type in (
+                    self.FixedProportion, self.FixedSize, self.Bootstrap):
                 remaining, sample = self.indices
                 self.outputInfoLabel.setText(
                     'Outputting %d instance%s.' %
                     (len(sample), "s" * (len(sample) != 1)))
-            else:
+            elif self.sampling_type == self.CrossValidation:
                 remaining, sample = self.indices[self.selectedFold - 1]
                 self.outputInfoLabel.setText(
                     'Outputting fold %d, %d instance%s.' %
@@ -215,16 +220,20 @@ def updateindices(self):
         num_classes = len(self.data.domain.class_var.values) \
             if self.data.domain.has_discrete_class else 0
 
+        size = None
         if self.sampling_type == self.FixedSize:
             size = self.sampleSizeNumber
             repl = self.replacement
         elif self.sampling_type == self.FixedProportion:
             size = np.ceil(self.sampleSizePercentage / 100 * data_length)
             repl = False
-        elif data_length < self.number_of_folds:
-            err_msg = "Number of folds exceeds the data size"
+        elif self.sampling_type == self.CrossValidation:
+            if data_length < self.number_of_folds:
+                err_msg = "Number of folds exceeds the data size"
+        else:
+            assert self.sampling_type == self.Bootstrap
 
-        if not repl and (data_length <= size):
+        if not repl and size is not None and (data_length <= size):
             err_msg = "Sample must be smaller than data"
         if not repl and data_length <= num_classes and self.stratify:
             err_msg = "Not enough data for stratified sampling"
@@ -241,13 +250,15 @@ def updateindices(self):
                       self.data.domain.has_discrete_class)
         if self.sampling_type == self.FixedSize:
             self.indices = sample_random_n(
-                self.data, self.sampleSizeNumber,
+                self.data, size,
                 stratified=stratified, replace=self.replacement,
                 random_state=rnd)
         elif self.sampling_type == self.FixedProportion:
             self.indices = sample_random_p(
                 self.data, self.sampleSizePercentage / 100,
                 stratified=stratified, random_state=rnd)
+        elif self.sampling_type == self.Bootstrap:
+            self.indices = sample_bootstrap(data_length, random_state=rnd)
         else:
             self.indices = sample_fold_indices(
                 self.data, self.number_of_folds, stratified=stratified,
@@ -332,6 +343,16 @@ def sample_random_p(table, p, stratified=False, random_state=None):
     return sample_random_n(table, n, stratified, False, random_state)
 
 
+def sample_bootstrap(size, random_state=None):
+    rgen = np.random.RandomState(random_state)
+    sample = rgen.randint(0, size, size)
+    sample.sort()  # not needed for the code below, just for the user
+    insample = np.ones((size,), dtype=np.bool)
+    insample[sample] = False
+    remaining = np.flatnonzero(insample)
+    return remaining, sample
+
+
 def test_main():
     app = QtGui.QApplication([])
     data = Table("iris")