def test_find_grid_close_to_image_edge(self):
"""
Create an image with a grid of 8 by 8 spots near the edge of the image. Then test if the spots are found
in the correct coordinates.
"""
# # set a grid of 8 by 8 points to 1 at the top left of the image
image = numpy.zeros((256, 256))
image[4:100:12, 4:100:12] = 1
spot_coordinates, translation, scaling, rotation, shear = spot.FindGridSpots(image, (8, 8))
# create a grid that contains the coordinates of the spots
xv = numpy.arange(4, 100, 12)
xx, yy = numpy.meshgrid(xv, xv)
grid = numpy.column_stack((xx.ravel(), yy.ravel()))
numpy.testing.assert_array_almost_equal(numpy.sort(spot_coordinates, axis=1), numpy.sort(grid, axis=1),
decimal=1)
# set a grid of 8 by 8 points to 1 at the bottom right of the image
image = numpy.zeros((256, 300))
image[168:253:12, 212:297:12] = 1
spot_coordinates, translation, scaling, rotation, shear = spot.FindGridSpots(image, (8, 8))
# create a grid that contains the coordinates of the spots
xv = numpy.arange(168, 253, 12)
yv = numpy.arange(212, 297, 12)
xx, yy = numpy.meshgrid(yv, xv)
grid = numpy.column_stack((xx.ravel(), yy.ravel()))
numpy.testing.assert_array_almost_equal(numpy.sort(spot_coordinates, axis=1), numpy.sort(grid, axis=1),
decimal=1)
def test_wrong_method(self):
"""Test that an error is raised when a wrong method is passed."""
image = numpy.zeros((256, 256))
# set a grid of 8 by 8 points to 1
image[54:150:12, 54:150:12] = 1
with self.assertRaises(ValueError):
spot.FindGridSpots(image, (8, 8), method='scaling')
def test_find_grid_similarity(self):
"""
Create an image with a grid of 8 by 8 spots. Then test if the spots are found in the correct coordinates and
that the rotation, scaling and translation are correct when using the similarity transformation method.
"""
image = numpy.zeros((256, 256))
# set a grid of 8 by 8 points to 1
image[54:150:12, 54:150:12] = 1
spot_coordinates, translation, scaling, rotation, shear = spot.FindGridSpots(
image, (8, 8), method=GRID_SIMILARITY)
self.assertAlmostEqual(rotation, 0, places=4)
self.assertIsNone(shear)
# create a grid that contains the coordinates of the spots
xv = numpy.arange(54, 150, 12)
xx, yy = numpy.meshgrid(xv, xv)
grid = numpy.column_stack((xx.ravel(), yy.ravel()))
numpy.testing.assert_array_almost_equal(numpy.sort(spot_coordinates,
axis=1),
numpy.sort(grid, axis=1),
decimal=2)
numpy.testing.assert_array_almost_equal(translation,
numpy.array([96, 96]),
decimal=3)
numpy.testing.assert_array_almost_equal(scaling,
numpy.array([12, 12]),
decimal=3)
def test_find_grid_on_image(self):
"""
Load an image with known spot coordinates, test if the spots are found in the correct coordinates and
that the rotation, scaling and translation are correct.
"""
grid_spots = numpy.load(os.path.join(TEST_IMAGE_PATH, "multiprobe01_grid_spots.npz"))
filename = os.path.join(TEST_IMAGE_PATH, "multiprobe01.tiff")
img = tiff.open_data(filename).content[0].getData()
spot_coordinates, translation, scaling, rotation, shear = spot.FindGridSpots(img, (14, 14))
numpy.testing.assert_array_almost_equal(spot_coordinates, grid_spots['spot_coordinates'])
numpy.testing.assert_array_almost_equal(translation, grid_spots['translation'], decimal=3)
numpy.testing.assert_array_almost_equal(scaling, grid_spots['scaling'], decimal=3)
self.assertAlmostEqual(rotation, grid_spots['rotation'])
def test_find_grid_with_shear(self):
"""
Create an images with grids of 3 by 2 spots. The grid in each image has a different amount of shear.
Test that the amount of shear found for each image is as expected.
"""
image_no_shear = numpy.array(
[[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0., 0., 0.],
[0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0., 0., 0.],
[0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]])
# Test that for an image without shear the shear and rotation are almost zero, when using the affine method.
*_, rotation, shear = spot.FindGridSpots(image_no_shear, (3, 2),
spot_size=4,
method=GRID_AFFINE)
self.assertAlmostEqual(rotation, 0, places=8)
self.assertAlmostEqual(shear, 0, places=8)
# Test that for an image without shear the rotation is almost zero,
# and shear is None when using the similarity method.
*_, rotation, shear = spot.FindGridSpots(image_no_shear, (3, 2),
spot_size=4,
method=GRID_SIMILARITY)
self.assertAlmostEqual(rotation, 0, places=8)
self.assertIsNone(shear)
image_shear = numpy.array(
[[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0., 0.],
[0., 0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0., 0., 0.],
[0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]])
image_more_shear = numpy.array(
[[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0.],
[0., 0., 0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0., 0., 0.],
[0., 0., 1., 1., 0., 0., 1., 1., 0., 0., 0., 1., 1., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]])
# Test that the image with more shear returns a higher absolute shear component, when using the affine method.
*_, shear = spot.FindGridSpots(image_shear, (3, 2),
spot_size=4,
method=GRID_AFFINE)
*_, more_shear = spot.FindGridSpots(image_more_shear, (3, 2),
spot_size=4,
method=GRID_AFFINE)
self.assertGreater(abs(more_shear), abs(shear))
# Since both images have a grid with shear, the shear in both cases should not be equal to zero.
self.assertNotEqual(shear, 0)
self.assertNotEqual(more_shear, 0)
