Merge pull request #5975 from ales-erjavec/feature-constructor-opt

[ENH] Feature constructor optimization

Author: VesnaT

Orange/data/variable.py

@@ -1,6 +1,7 @@
 import re
 import warnings
 from collections.abc import Iterable
+from typing import Sequence
 
 from datetime import datetime, timedelta, timezone
 from numbers import Number, Real, Integral
@@ -168,6 +169,44 @@ def __new__(cls, variable, value=Unknown):
             self._value = value
         return self
 
+    @staticmethod
+    def _as_values_primitive(variable, data) -> Sequence['Value']:
+        assert variable.is_primitive()
+        _Value = Value
+        _float_new = float.__new__
+        res = [Value(variable, np.nan)] * len(data)
+        for i, v in enumerate(data):
+            v = _float_new(_Value, v)
+            v.variable = variable
+            res[i] = v
+        return res
+
+    @staticmethod
+    def _as_values_non_primitive(variable, data) -> Sequence['Value']:
+        assert not variable.is_primitive()
+        _Value = Value
+        _float_new = float.__new__
+        data_arr = np.array(data, dtype=object)
+        NA = data_arr == variable.Unknown
+        fdata = np.full(len(data), np.finfo(float).min)
+        fdata[NA] = np.nan
+        res = [Value(variable, Variable.Unknown)] * len(data)
+        for i, (v, fval) in enumerate(zip(data, fdata)):
+            val = _float_new(_Value, fval)
+            val.variable = variable
+            val._value = v
+            res[i] = val
+        return res
+
+    @staticmethod
+    def _as_values(variable, data):
+        """Equivalent but faster then `[Value(variable, v) for v in data]
+        """
+        if variable.is_primitive():
+            return Value._as_values_primitive(variable, data)
+        else:
+            return Value._as_values_non_primitive(variable, data)
+
     def __init__(self, _, __=Unknown):
         # __new__ does the job, pylint: disable=super-init-not-called
         pass

Orange/tests/test_value.py

@@ -64,3 +64,13 @@ def test_hash(self):
         self.assertTrue(val == v and hash(val) == hash(v))
         val = Value(DiscreteVariable("var", ["red", "green", "blue"]), 1)
         self.assertRaises(TypeError, hash, val)
+
+    def test_as_values(self):
+        x = ContinuousVariable("x")
+        values = Value._as_values(x, [0., 1., 2.])  # pylint: disable=protected-access
+        self.assertIsInstance(values[0], Value)
+        self.assertEqual(values[0], 0)
+        s = StringVariable("s")
+        values = Value._as_values(s, ["a", "b", ""])  # pylint: disable=protected-access
+        self.assertIsInstance(values[0], Value)
+        self.assertEqual(values[0], "a")

Orange/widgets/data/oweditdomain.py

@@ -40,7 +40,7 @@
 
 from Orange.preprocess.transformation import Transformation, Identity, Lookup
 from Orange.widgets import widget, gui, settings
-from Orange.widgets.utils import itemmodels
+from Orange.widgets.utils import itemmodels, ftry
 from Orange.widgets.utils.buttons import FixedSizeButton
 from Orange.widgets.utils.itemmodels import signal_blocking
 from Orange.widgets.utils.widgetpreview import WidgetPreview
@@ -50,8 +50,6 @@
 MArray = np.ma.MaskedArray
 DType = Union[np.dtype, type]
 
-A = TypeVar("A")  # pylint: disable=invalid-name
-B = TypeVar("B")  # pylint: disable=invalid-name
 V = TypeVar("V", bound=Orange.data.Variable)  # pylint: disable=invalid-name
 H = TypeVar("H", bound=Hashable)  # pylint: disable=invalid-name
 
@@ -2631,21 +2629,6 @@ def apply_transform_string(var, trs):
     return variable
 
 
-def ftry(
-        func: Callable[..., A],
-        error: Union[Type[BaseException], Tuple[Type[BaseException]]],
-        default: B
-) -> Callable[..., Union[A, B]]:
-    """
-    Wrap a `func` such that if `errors` occur `default` is returned instead."""
-    def wrapper(*args, **kwargs):
-        try:
-            return func(*args, **kwargs)
-        except error:
-            return default
-    return wrapper
-
-
 class DictMissingConst(dict):
     """
     `dict` with a constant for `__missing__()` value.

Orange/widgets/data/owfeatureconstructor.py

@@ -18,7 +18,7 @@
 
 from traceback import format_exception_only
 from collections import namedtuple, OrderedDict
-from itertools import chain, count
+from itertools import chain, count, starmap
 from typing import List, Dict, Any
 
 import numpy as np
@@ -32,15 +32,19 @@
 from orangewidget.utils.combobox import ComboBoxSearch
 
 import Orange
+from Orange.data import Variable, Table, Value, Instance
 from Orange.data.util import get_unique_names
 from Orange.widgets import gui
 from Orange.widgets.settings import ContextSetting, DomainContextHandler
-from Orange.widgets.utils import itemmodels, vartype
+from Orange.widgets.utils import (
+    itemmodels, vartype, ftry, unique_everseen as unique
+)
 from Orange.widgets.utils.sql import check_sql_input
 from Orange.widgets import report
 from Orange.widgets.utils.widgetpreview import WidgetPreview
 from Orange.widgets.widget import OWWidget, Msg, Input, Output
 
+
 FeatureDescriptor = \
     namedtuple("FeatureDescriptor", ["name", "expression"])
 
@@ -729,11 +733,14 @@ def duplicateFeature(self):
 
     @staticmethod
     def check_attrs_values(attr, data):
-        for i in range(len(data)):
-            for var in attr:
-                if not math.isnan(data[i, var]) \
-                        and int(data[i, var]) >= len(var.values):
-                    return var.name
+        for var in attr:
+            col, _ = data.get_column_view(var)
+            mask = ~np.isnan(col)
+            grater_or_equal = np.greater_equal(
+                col, len(var.values), out=mask, where=mask
+            )
+            if grater_or_equal.any():
+                return var.name
         return None
 
     def _validate_descriptors(self, desc):
@@ -1162,25 +1169,59 @@ def __init__(self, expression, args, extra_env=None, cast=None, use_values=False
         self.mask_exceptions = True
         self.use_values = use_values
 
-    def __call__(self, instance, *_):
-        if isinstance(instance, Orange.data.Table):
-            return [self(inst) for inst in instance]
+    def __call__(self, table, *_):
+        if isinstance(table, Table):
+            return self.__call_table(table)
         else:
-            try:
-                args = [str(instance[var]) if var.is_string
-                    else var.values[int(instance[var])] if var.is_discrete and not self.use_values
-                    else instance[var]
-                    for _, var in self.args]
-                y = self.func(*args)
-            # user's expression can contain arbitrary errors
-            # this also covers missing attributes
-            except:  # pylint: disable=bare-except
-                if not self.mask_exceptions:
-                    raise
-                return np.nan
-            if self.cast:
-                y = self.cast(y)
-            return y
+            return self.__call_instance(table)
+
+    def __call_table(self, table):
+        try:
+            cols = [self.extract_column(table, var) for _, var in self.args]
+        except ValueError:
+            if self.mask_exceptions:
+                return np.full(len(table), np.nan)
+            else:
+                raise
+
+        if not cols:
+            args = [()] * len(table)
+        else:
+            args = zip(*cols)
+        f = self.func
+        if self.mask_exceptions:
+            y = list(starmap(ftry(f, Exception, np.nan), args))
+        else:
+            y = list(starmap(f, args))
+        if self.cast is not None:
+            cast = self.cast
+            y = [cast(y_) for y_ in y]
+        return y
+
+    def __call_instance(self, instance: Instance):
+        table = Table.from_numpy(
+            instance.domain,
+            np.array([instance.x]),
+            np.array([instance.y]),
+            np.array([instance.metas]),
+        )
+        return self.__call_table(table)[0]
+
+    def extract_column(self, table: Table, var: Variable):
+        data, _ = table.get_column_view(var)
+        if var.is_string:
+            return list(map(var.str_val, data))
+        elif var.is_discrete and not self.use_values:
+            values = np.array([*var.values, None], dtype=object)
+            idx = data.astype(int)
+            idx[~np.isfinite(data)] = len(values) - 1
+            return values[idx].tolist()
+        elif var.is_time:  # time always needs Values due to str(val) formatting
+            return Value._as_values(var, data.tolist())  # pylint: disable=protected-access
+        elif not self.use_values:
+            return data.tolist()
+        else:
+            return Value._as_values(var, data.tolist())  # pylint: disable=protected-access
 
     def __reduce__(self):
         return type(self), (self.expression, self.args,
@@ -1190,15 +1231,5 @@ def __repr__(self):
         return "{0.__name__}{1!r}".format(*self.__reduce__())
 
 
-def unique(seq):
-    seen = set()
-    unique_el = []
-    for el in seq:
-        if el not in seen:
-            unique_el.append(el)
-            seen.add(el)
-    return unique_el
-
-
 if __name__ == "__main__":  # pragma: no cover
     WidgetPreview(OWFeatureConstructor).run(Orange.data.Table("iris"))

Orange/widgets/data/tests/test_owfeatureconstructor.py

@@ -305,6 +305,12 @@ def test_missing_variable(self):
         self.assertTrue(np.all(np.isnan(r)))
         self.assertTrue(np.isnan(f(data2[0])))
 
+    def test_time_str(self):
+        data = Table.from_numpy(Domain([TimeVariable("T", have_date=True)]), [[0], [0]])
+        f = FeatureFunc("str(T)", [("T", data.domain[0])])
+        c = f(data)
+        self.assertEqual(c, ["1970-01-01", "1970-01-01"])
+
     def test_invalid_expression_variable(self):
         iris = Table("iris")
         f = FeatureFunc("1 / petal_length",

Orange/widgets/utils/__init__.py

@@ -3,7 +3,7 @@
 import sys
 from collections import deque
 from typing import (
-    TypeVar, Callable, Any, Iterable, Optional, Hashable, Type, Union
+    TypeVar, Callable, Any, Iterable, Optional, Hashable, Type, Union, Tuple
 )
 from xml.sax.saxutils import escape
 
@@ -92,6 +92,8 @@ def qname(type_: type) -> str:
 
 _T1 = TypeVar("_T1")  # pylint: disable=invalid-name
 _E = TypeVar("_E", bound=enum.Enum)  # pylint: disable=invalid-name
+_A = TypeVar("_A")  # pylint: disable=invalid-name
+_B = TypeVar("_B")  # pylint: disable=invalid-name
 
 
 def apply_all(seq, op):
@@ -101,6 +103,22 @@ def apply_all(seq, op):
     deque(map(op, seq), maxlen=0)
 
 
+def ftry(
+        func: Callable[..., _A],
+        error: Union[Type[BaseException], Tuple[Type[BaseException]]],
+        default: _B
+) -> Callable[..., Union[_A, _B]]:
+    """
+    Wrap a `func` such that if `errors` occur `default` is returned instead.
+    """
+    def wrapper(*args, **kwargs):
+        try:
+            return func(*args, **kwargs)
+        except error:
+            return default
+    return wrapper
+
+
 def unique_everseen(iterable, key=None):
     # type: (Iterable[_T1], Optional[Callable[[_T1], Hashable]]) -> Iterable[_T1]
     """