Merge pull request #98 from industrial-sloth/data_getter

Data getter

Author: freeman-lab

python/test/test_data.py

@@ -0,0 +1,257 @@
+from nose.tools import assert_equals, assert_is_none, assert_raises, assert_true
+from numpy import array, array_equal
+
+from thunder.rdds.data import Data
+from test_utils import PySparkTestCase
+
+
+class TestImagesGetters(PySparkTestCase):
+    """Test `get` and related methods on an Images-like Data object
+    """
+    def setUp(self):
+        super(TestImagesGetters, self).setUp()
+        self.ary1 = array([[1, 2], [3, 4]], dtype='int16')
+        self.ary2 = array([[5, 6], [7, 8]], dtype='int16')
+        rdd = self.sc.parallelize([(0, self.ary1), (1, self.ary2)])
+        self.images = Data(rdd, dtype='int16')
+
+    def test_getMissing(self):
+        assert_is_none(self.images.get(-1))
+
+    def test_get(self):
+        assert_true(array_equal(self.ary2, self.images.get(1)))
+
+        # keys are integers, ask for sequence
+        assert_raises(ValueError, self.images.get, (1, 2))
+
+    def test_getMany(self):
+        vals = self.images.getMany([0, -1, 1, 0])
+        assert_equals(4, len(vals))
+        assert_true(array_equal(self.ary1, vals[0]))
+        assert_is_none(vals[1])
+        assert_true(array_equal(self.ary2, vals[2]))
+        assert_true(array_equal(self.ary1, vals[3]))
+
+        # keys are integers, ask for sequences:
+        assert_raises(ValueError, self.images.get, [(0, 0)])
+        assert_raises(ValueError, self.images.get, [0, (0, 0), 1, 0])
+
+    def test_getRanges(self):
+        vals = self.images.getRange(slice(None))
+        assert_equals(2, len(vals))
+        assert_equals(0, vals[0][0])
+        assert_equals(1, vals[1][0])
+        assert_true(array_equal(self.ary1, vals[0][1]))
+        assert_true(array_equal(self.ary2, vals[1][1]))
+
+        vals = self.images.getRange(slice(0, 1))
+        assert_equals(1, len(vals))
+        assert_equals(0, vals[0][0])
+        assert_true(array_equal(self.ary1, vals[0][1]))
+
+        vals = self.images.getRange(slice(1))
+        assert_equals(1, len(vals))
+        assert_equals(0, vals[0][0])
+        assert_true(array_equal(self.ary1, vals[0][1]))
+
+        vals = self.images.getRange(slice(1, 2))
+        assert_equals(1, len(vals))
+        assert_equals(1, vals[0][0])
+        assert_true(array_equal(self.ary2, vals[0][1]))
+
+        vals = self.images.getRange(slice(2, 3))
+        assert_equals(0, len(vals))
+
+        # keys are integers, ask for sequence
+        assert_raises(ValueError, self.images.getRange, [slice(1), slice(1)])
+
+        # raise exception if 'step' specified:
+        assert_raises(ValueError, self.images.getRange, slice(1, 2, 2))
+
+    def test_brackets(self):
+        vals = self.images[1]
+        assert_true(array_equal(self.ary2, vals))
+
+        vals = self.images[0:1]
+        assert_equals(1, len(vals))
+        assert_equals(0, vals[0][0])
+        assert_true(array_equal(self.ary1, vals[0][1]))
+
+        vals = self.images[:]
+        assert_equals(2, len(vals))
+        assert_equals(0, vals[0][0])
+        assert_equals(1, vals[1][0])
+        assert_true(array_equal(self.ary1, vals[0][1]))
+        assert_true(array_equal(self.ary2, vals[1][1]))
+
+        vals = self.images[1:4]
+        assert_equals(1, len(vals))
+        assert_equals(1, vals[0][0])
+        assert_true(array_equal(self.ary2, vals[0][1]))
+
+        vals = self.images[1:]
+        assert_equals(1, len(vals))
+        assert_equals(1, vals[0][0])
+        assert_true(array_equal(self.ary2, vals[0][1]))
+
+        vals = self.images[:1]
+        assert_equals(1, len(vals))
+        assert_equals(0, vals[0][0])
+        assert_true(array_equal(self.ary1, vals[0][1]))
+
+        assert_is_none(self.images[2])
+
+        assert_equals([], self.images[2:3])
+
+
+class TestSeriesGetters(PySparkTestCase):
+    """Test `get` and related methods on a Series-like Data object
+    """
+    def setUp(self):
+        super(TestSeriesGetters, self).setUp()
+        self.dataLocal = [
+            ((0, 0), array([1.0, 2.0, 3.0], dtype='float32')),
+            ((0, 1), array([2.0, 2.0, 4.0], dtype='float32')),
+            ((1, 0), array([4.0, 2.0, 1.0], dtype='float32')),
+            ((1, 1), array([3.0, 1.0, 1.0], dtype='float32'))
+        ]
+        self.series = Data(self.sc.parallelize(self.dataLocal), dtype='float32')
+
+    def test_getMissing(self):
+        assert_is_none(self.series.get((-1, -1)))
+
+    def test_get(self):
+        expected = self.dataLocal[1][1]
+        assert_true(array_equal(expected, self.series.get((0, 1))))
+
+        assert_raises(ValueError, self.series.get, 1)  # keys are sequences, ask for integer
+        assert_raises(ValueError, self.series.get, (1, 2, 3))  # key length mismatch
+
+    def test_getMany(self):
+        vals = self.series.getMany([(0, 0), (17, 256), (1, 0), (0, 0)])
+        assert_equals(4, len(vals))
+        assert_true(array_equal(self.dataLocal[0][1], vals[0]))
+        assert_is_none(vals[1])
+        assert_true(array_equal(self.dataLocal[2][1], vals[2]))
+        assert_true(array_equal(self.dataLocal[0][1], vals[3]))
+
+        assert_raises(ValueError, self.series.getMany, [1])  # keys are sequences, ask for integer
+        assert_raises(ValueError, self.series.getMany, [(0, 0), 1, (1, 0), (0, 0)])  # asking for integer again
+
+    def test_getRanges(self):
+        vals = self.series.getRange([slice(2), slice(2)])
+        assert_equals(4, len(vals))
+        assert_equals(self.dataLocal[0][0], vals[0][0])
+        assert_equals(self.dataLocal[1][0], vals[1][0])
+        assert_equals(self.dataLocal[2][0], vals[2][0])
+        assert_equals(self.dataLocal[3][0], vals[3][0])
+        assert_true(array_equal(self.dataLocal[0][1], vals[0][1]))
+        assert_true(array_equal(self.dataLocal[1][1], vals[1][1]))
+        assert_true(array_equal(self.dataLocal[2][1], vals[2][1]))
+        assert_true(array_equal(self.dataLocal[3][1], vals[3][1]))
+
+        vals = self.series.getRange([slice(2), slice(1)])
+        assert_equals(2, len(vals))
+        assert_equals(self.dataLocal[0][0], vals[0][0])
+        assert_equals(self.dataLocal[2][0], vals[1][0])
+        assert_true(array_equal(self.dataLocal[0][1], vals[0][1]))
+        assert_true(array_equal(self.dataLocal[2][1], vals[1][1]))
+
+        vals = self.series.getRange([slice(None), slice(1, 2)])
+        assert_equals(2, len(vals))
+        assert_equals(self.dataLocal[1][0], vals[0][0])
+        assert_equals(self.dataLocal[3][0], vals[1][0])
+        assert_true(array_equal(self.dataLocal[1][1], vals[0][1]))
+        assert_true(array_equal(self.dataLocal[3][1], vals[1][1]))
+
+        vals = self.series.getRange([slice(None), slice(None)])
+        assert_equals(4, len(vals))
+        assert_equals(self.dataLocal[0][0], vals[0][0])
+        assert_equals(self.dataLocal[1][0], vals[1][0])
+        assert_equals(self.dataLocal[2][0], vals[2][0])
+        assert_equals(self.dataLocal[3][0], vals[3][0])
+        assert_true(array_equal(self.dataLocal[0][1], vals[0][1]))
+        assert_true(array_equal(self.dataLocal[1][1], vals[1][1]))
+        assert_true(array_equal(self.dataLocal[2][1], vals[2][1]))
+        assert_true(array_equal(self.dataLocal[3][1], vals[3][1]))
+
+        vals = self.series.getRange([0, slice(None)])
+        assert_equals(2, len(vals))
+        assert_equals(self.dataLocal[0][0], vals[0][0])
+        assert_equals(self.dataLocal[1][0], vals[1][0])
+        assert_true(array_equal(self.dataLocal[0][1], vals[0][1]))
+        assert_true(array_equal(self.dataLocal[1][1], vals[1][1]))
+
+        vals = self.series.getRange([0, 1])
+        assert_equals(1, len(vals))
+        assert_equals(self.dataLocal[1][0], vals[0][0])
+        assert_true(array_equal(self.dataLocal[1][1], vals[0][1]))
+
+        vals = self.series.getRange([slice(2, 3), slice(None)])
+        assert_equals(0, len(vals))
+
+        # keys are sequences, ask for single slice
+        assert_raises(ValueError, self.series.getRange, slice(2, 3))
+
+        # ask for wrong number of slices
+        assert_raises(ValueError, self.series.getRange, [slice(2, 3), slice(2, 3), slice(2, 3)])
+
+        # raise exception if 'step' specified:
+        assert_raises(ValueError, self.series.getRange, [slice(0, 4, 2), slice(2, 3)])
+
+    def test_brackets(self):
+        # returns just value; calls `get`
+        vals = self.series[(1, 0)]
+        assert_true(array_equal(self.dataLocal[2][1], vals))
+
+        # tuple isn't needed; returns just value, calls `get`
+        vals = self.series[0, 1]
+        assert_true(array_equal(self.dataLocal[1][1], vals))
+
+        # if slices are passed, calls `getRange`, returns keys and values
+        vals = self.series[0:1, 1:2]
+        assert_equals(1, len(vals))
+        assert_equals(self.dataLocal[1][0], vals[0][0])
+        assert_true(array_equal(self.dataLocal[1][1], vals[0][1]))
+
+        # if slice extends out of bounds, return only the elements that are in bounds
+        vals = self.series[:4, :1]
+        assert_equals(2, len(vals))
+        assert_equals(self.dataLocal[0][0], vals[0][0])
+        assert_equals(self.dataLocal[2][0], vals[1][0])
+        assert_true(array_equal(self.dataLocal[0][1], vals[0][1]))
+        assert_true(array_equal(self.dataLocal[2][1], vals[1][1]))
+
+        # empty slice works
+        vals = self.series[:, 1:2]
+        assert_equals(2, len(vals))
+        assert_equals(self.dataLocal[1][0], vals[0][0])
+        assert_equals(self.dataLocal[3][0], vals[1][0])
+        assert_true(array_equal(self.dataLocal[1][1], vals[0][1]))
+        assert_true(array_equal(self.dataLocal[3][1], vals[1][1]))
+
+        # multiple empty slices work
+        vals = self.series[:, :]
+        assert_equals(4, len(vals))
+        assert_equals(self.dataLocal[0][0], vals[0][0])
+        assert_equals(self.dataLocal[1][0], vals[1][0])
+        assert_equals(self.dataLocal[2][0], vals[2][0])
+        assert_equals(self.dataLocal[3][0], vals[3][0])
+        assert_true(array_equal(self.dataLocal[0][1], vals[0][1]))
+        assert_true(array_equal(self.dataLocal[1][1], vals[1][1]))
+        assert_true(array_equal(self.dataLocal[2][1], vals[2][1]))
+        assert_true(array_equal(self.dataLocal[3][1], vals[3][1]))
+
+        # mixing slices and individual indicies works:
+        vals = self.series[0, :]
+        assert_equals(2, len(vals))
+        assert_equals(self.dataLocal[0][0], vals[0][0])
+        assert_equals(self.dataLocal[1][0], vals[1][0])
+        assert_true(array_equal(self.dataLocal[0][1], vals[0][1]))
+        assert_true(array_equal(self.dataLocal[1][1], vals[1][1]))
+
+        # trying to getitem a key that doesn't exist returns None
+        assert_is_none(self.series[(25, 17)])
+
+        # passing a range that is completely out of bounds returns []
+        assert_equals([], self.series[2:3, :])

python/test/test_images.py

@@ -4,7 +4,7 @@
 from numpy import allclose, arange, array, array_equal, prod, squeeze, zeros
 from numpy import dtype as dtypeFunc
 import itertools
-from nose.tools import assert_equals, assert_raises, assert_true
+from nose.tools import assert_equals, assert_is_none, assert_raises, assert_true
 import unittest
 
 from thunder.rdds.fileio.imagesloader import ImagesLoader

python/test/test_series.py

@@ -1,6 +1,6 @@
 from numpy import allclose, amax, arange, array, array_equal
 from numpy import dtype as dtypeFunc
-from nose.tools import assert_equals, assert_true, assert_raises
+from nose.tools import assert_equals, assert_is_none, assert_raises, assert_true
 
 from thunder.rdds.series import Series
 from test_utils import *
@@ -305,4 +305,3 @@ def setIndex(data, idx):
 
         assert_raises(ValueError, setIndex, data, 5)
         assert_raises(ValueError, setIndex, data, [1, 2])
-