def test_get_tile(self):
tile_size = 10
tiler = Tiler(data_shape=self.data.shape, tile_shape=(tile_size, ))
with self.assertRaises(IndexError):
tiler.get_tile(self.data, len(tiler))
with self.assertRaises(IndexError):
tiler.get_tile(self.data, -1)
# copy test
t = tiler.get_tile(self.data, 0, copy_data=True)
t[9] = 0
np.testing.assert_equal([0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
tiler.get_tile(self.data, 0))
np.testing.assert_equal([0, 1, 2, 3, 4, 5, 6, 7, 8, 0], t)
t = tiler.get_tile(self.data, 0, copy_data=False)
t[9] = 0
np.testing.assert_equal([0, 1, 2, 3, 4, 5, 6, 7, 8, 0],
tiler.get_tile(self.data, 0))
np.testing.assert_equal([0, 1, 2, 3, 4, 5, 6, 7, 8, 0], t)
t[9] = 9
# test callable data
fn = lambda x, w: self.data[x:x + w]
t = tiler.get_tile(fn, 0)
np.testing.assert_equal([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], t)
t = tiler.get_tile(fn, 1)
np.testing.assert_equal([10, 11, 12, 13, 14, 15, 16, 17, 18, 19], t)
def test_iterator(self):
tile_size = 10
tiler = Tiler(data_shape=self.data.shape, tile_shape=(tile_size, ))
# copy test with iterator
t = list(tiler(self.data, copy_data=True))
t[0][1][9] = 0
np.testing.assert_equal([0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
tiler.get_tile(self.data, 0))
np.testing.assert_equal([0, 1, 2, 3, 4, 5, 6, 7, 8, 0], t[0][1])
self.assertNotEqual(t[0][1][9], self.data[9])
t = [tile for _, tile in tiler(self.data, copy_data=False)]
t[0][9] = 0
np.testing.assert_equal([0, 1, 2, 3, 4, 5, 6, 7, 8, 0],
tiler.get_tile(self.data, 0))
np.testing.assert_equal([0, 1, 2, 3, 4, 5, 6, 7, 8, 0], t[0])
self.assertEqual(t[0][9], self.data[9])
# test batch size
with self.assertRaises(ValueError):
t = [x for _, x in tiler(self.data, batch_size=-1)]
t = [x for _, x in tiler(self.data, batch_size=0)]
self.assertEqual(len(t), 10)
np.testing.assert_equal(t[0].shape, (10, ))
t = [x for _, x in tiler(self.data, batch_size=1)]
self.assertEqual(len(t), 10)
np.testing.assert_equal(t[0].shape, (1, 10))
t = [x for _, x in tiler(self.data, batch_size=10)]
self.assertEqual(len(t), 1)
np.testing.assert_equal(t[0].shape, (10, 10))
t = [x for _, x in tiler(self.data, batch_size=9)]
self.assertEqual(len(t), 2)
np.testing.assert_equal(t[0].shape, (9, 10))
np.testing.assert_equal(t[1].shape, (1, 10))
t = [x for _, x in tiler(self.data, batch_size=9, drop_last=True)]
self.assertEqual(len(t), 1)
np.testing.assert_equal(t[0].shape, (9, 10))
def test_callable_data(self):
def fn(*x):
raise ValueError(x)
# 1D test
tiler = Tiler(data_shape=(100, ), tile_shape=(10, ))
for i in range(tiler.n_tiles):
with self.assertRaises(ValueError) as cm:
tiler.get_tile(fn, i)
np.testing.assert_equal(
cm.exception.args[0],
(*tiler.get_tile_bbox_position(i)[0], *tiler.tile_shape))
# 2D test
tiler = Tiler(data_shape=(100, 100), tile_shape=(10, 20))
for i in range(tiler.n_tiles):
with self.assertRaises(ValueError) as cm:
tiler.get_tile(fn, i)
np.testing.assert_equal(
cm.exception.args[0],
(*tiler.get_tile_bbox_position(i)[0], *tiler.tile_shape))
# 3D test
tiler = Tiler(data_shape=(100, 100, 100), tile_shape=(10, 20, 50))
for i in range(tiler.n_tiles):
with self.assertRaises(ValueError) as cm:
tiler.get_tile(fn, i)
np.testing.assert_equal(
cm.exception.args[0],
(*tiler.get_tile_bbox_position(i)[0], *tiler.tile_shape))
# channel dimension test
tiler = Tiler(data_shape=(100, 100, 3),
tile_shape=(10, 20, 3),
channel_dimension=2)
for i in range(tiler.n_tiles):
with self.assertRaises(ValueError) as cm:
tiler.get_tile(fn, i)
np.testing.assert_equal(
cm.exception.args[0],
(*tiler.get_tile_bbox_position(i, with_channel_dim=True)[0],
*tiler.tile_shape))
def test_add(self):
tiler = Tiler(data_shape=self.data.shape, tile_shape=(10, ))
tiler2 = Tiler(data_shape=self.data.shape,
tile_shape=(12, ),
mode='irregular')
tiler3 = Tiler(data_shape=(3, ) + self.data.shape,
tile_shape=(
3,
10,
),
channel_dimension=0)
merger = Merger(tiler)
merger_logits = Merger(tiler, logits=3)
merger_irregular = Merger(tiler2)
merger_channel_dim = Merger(tiler3)
tile = tiler.get_tile(self.data, 0)
tile_logits = np.vstack((tile, tile, tile))
tile_irregular = tiler2.get_tile(self.data, len(tiler2) - 1)
# Wrong tile id cases
with self.assertRaises(IndexError):
merger.add(-1, np.ones((10, )))
with self.assertRaises(IndexError):
merger.add(len(tiler), np.ones((10, )))
# Usual mergers expect tile_shape == data_shape
with self.assertRaises(ValueError):
merger.add(0, np.ones((
3,
10,
)))
merger.add(0, tile)
np.testing.assert_equal(merger.merge()[:10], tile)
# Logits merger expects an extra dimension in front for logits
with self.assertRaises(ValueError):
merger_logits.add(0, np.ones((10, )))
merger_logits.add(0, tile_logits)
np.testing.assert_equal(merger_logits.merge()[:, :10], tile_logits)
np.testing.assert_equal(
merger_logits.merge(argmax=True)[:10], np.zeros((10, )))
# Irregular merger expects all(data_shape <= tile_shape)
with self.assertRaises(ValueError):
merger_irregular.add(0, np.ones((13, )))
merger_irregular.add(len(tiler2) - 1, tile_irregular)
np.testing.assert_equal(
merger_irregular.merge()[-len(tile_irregular):], tile_irregular)
# Channel dimension merger
with self.assertRaises(ValueError):
merger_channel_dim.add(0, np.ones((10, )))
merger_channel_dim.add(0, tile_logits)
np.testing.assert_equal(merger_channel_dim.merge()[:, :10],
tile_logits)
# gotta get that 100% coverage
# this should just print a warning
# let's suppress it to avoid confusion
with open(os.devnull, "w") as null:
with redirect_stderr(null):
merger.set_window('boxcar')
