def test_clear_mask(self, patch_data_ones):
"""
Test clearing the mask
Args:
patch_data_ones: Image data
Test Condition:
The mask is all zero's
"""
patch = Patch(patch_data_ones, (2, 3))
patch.clear_mask()
assert not np.any(patch.mask)
def test_set_mask(self, patch_data_zeros, patch_data_many_components):
"""
Test setting the mask
Args:
patch_data_zeros: Image data with all zeros
Test Condition:
The mask property is set to the given mask
"""
patch = Patch(patch_data_zeros, (5, 6))
patch.mask = patch_data_many_components
np.testing.assert_equal(
np.any(np.equal(patch_data_many_components, patch.mask)), True)
def test_apply_threshold_invalid(self, test_image_data):
"""
Test applying and invalid threshold.
Args:
test_image_data: Imag data for testing, a numpy array
Test Condition:
Raises ValueError
"""
patch_data = test_image_data[:70, :130]
patch = Patch(patch_data, (1, 4))
with pytest.raises(ValueError):
patch._apply_threshold(7)
def test_flood_remove_region_old_pos(self, patch_data_ones,
patch_data_many_components):
"""
Test using flood remove with an old position.
Args:
patch_data_ones: Image data with all zeros
patch_data_many_components: Image data with many connected
components.
Test Condition:
The mask at the given position is 0
"""
position = (patch_data_ones.shape[0] // 2,
patch_data_ones.shape[1] // 2)
tolerance = 0.0001
patch = Patch(patch_data_many_components, (7, 3))
patch.mask = patch_data_ones
patch._old_flood_remove_position = position
patch._old_mask = patch_data_ones
patch.flood_remove_region(position, tolerance)
assert patch.mask[position[0], position[1]] == 0
def test_get_circle(self, patch_data_ones):
"""
Test getting a circle.
Args:
patch_data_ones: Image data all ones
Test Condition:
Returns correct coordinate lists.
"""
patch = Patch(patch_data_ones, (4, 3))
position = (2, 2)
radius = 2
expected_rr = [1, 1, 1, 2, 2, 2, 3, 3, 3]
expected_cc = [1, 2, 3, 1, 2, 3, 1, 2, 3]
rr, cc = patch._get_circle(position, radius)
assert rr == expected_rr
assert cc == expected_cc
position = (0, 0)
radius = 2
expected_rr = [0, 0, 1, 1]
expected_cc = [0, 1, 0, 1]
x, y = patch_data_ones.shape[0], patch_data_ones.shape[1]
position = (x, y)
radius = 2
expected_rr = [x - 1]
expected_cc = [y - 1]
rr, cc = patch._get_circle(position, radius)
assert rr == expected_rr
assert cc == expected_cc
def test_threshold_valid(self, test_image_data):
"""
Test setting the threshold with a value between 0 and 1
Test Condition:
self.threshold is set to the value
The mask is changed
"""
patch_data = test_image_data[:100, :100]
patch = Patch(patch_data, (1, 1))
old_mask = np.copy(patch.mask)
patch.threshold = 0.7
assert patch.threshold == 0.7
np.testing.assert_equal(np.any(np.not_equal(old_mask, patch.mask)),
True)
def test_apply_threshold(self, test_image_data):
"""
Test applying a valid threshold
Args:
test_image_data: Image data for testing, a numpy array
Test Condition:
The mask is changed
"""
patch_data = test_image_data[:130, :100]
patch = Patch(patch_data, (1, 2))
old_mask = np.copy(patch.mask)
patch._apply_threshold(0.3)
np.testing.assert_equal(np.any(np.not_equal(old_mask, patch.mask)),
True)
def test_flood_add_region_new_pos(self, patch_data_zeros,
patch_data_many_components):
"""
Test using flood add with a new position.
Args:
patch_data_zeros: Image data with all zeros
patch_data_many_components: Image data with many connected
components
Test Condition:
The mask at the given position is 1
"""
position = (patch_data_zeros.shape[0] // 2,
patch_data_zeros.shape[1] // 2)
tolerance = 0.0001
patch = Patch(patch_data_many_components, (7, 3))
patch.mask = patch_data_zeros
patch._old_flood_add_position = (0, 0)
patch.flood_add_region(position, tolerance)
assert patch.mask[position[0], position[1]] == 1
def test_threshold_invalid(self, test_image_data):
"""
Test setting the threshold to a value above 1
Args:
test_image_data: Image data for testing
Test Condition:
The threshold does not change
The mask is the same
"""
patch_data = test_image_data[:100, :100]
patch = Patch(patch_data, (1, 1))
old_mask = np.copy(patch.mask)
old_thresh = patch.threshold
patch.threshold = 1.2
assert patch.threshold == old_thresh
np.testing.assert_equal(np.any(np.not_equal(old_mask, patch.mask)),
False)
def test_overlay_mask(self, test_image_data, patch_data_ones):
"""
Test overlaying the mask on the image.
Args:
test_image_data: Image data for testing
patch_data_ones: Image data all ones.
Test Condition:
overlay_image is a numpy array with the same shape as the
patch
"""
img = test_image_data[:patch_data_ones.shape[0], :patch_data_ones.
shape[1]]
patch = Patch(img, (2, 3))
patch.mask = patch_data_ones
patch._overlay_mask()
assert patch.overlay_image.shape[:2] == patch.patch.shape
def test_get_patch_index(self, patch_data_zeros):
"""
Test getting the patch index
Args:
patch_data_zeros: Image data with all zeros
Test Condition:
The correct patch index is returned
"""
patch = Patch(patch_data_zeros, (4, 5))
assert patch.patch_index == (4, 5)
def test_init_all_black(self, patch_data_zeros):
"""
Test making a patch where the image is all black and threshold_otsu
fails.
Args:
patch_data_zeros: A numpy array of all zero image data
Test Condition:
The threshold is set to 1
"""
patch = Patch(patch_data_zeros, (2, 3))
assert patch.threshold == 1
def test_remove_region(self, patch_data_ones):
"""
Test removing a region.
Args:
patch_data_ones: Image data containing all ones
Test Condition:
The points in the mask at the given position are set to 0
"""
patch = Patch(patch_data_ones, (4, 4))
patch._mask = patch_data_ones
position = (5, 5)
radius = 3
patch.remove_region(position, radius)
rr, cc = patch._get_circle(position, radius)
assert np.all(patch.mask[rr, cc] == 0)
def test_remove_landmark(self, patch_data_ones):
"""
Test removing pixels that were marked as landmarks
Args:
patch_data_ones: Image data
Test Condition:
The pixels in the given area are labelled as 0
"""
patch = Patch(patch_data_ones, (3, 4))
patch._landmark_labels = patch_data_ones
position = (5, 5)
radius = 3
patch.remove_landmark(position, radius)
rr, cc = patch._get_circle(position, radius)
assert np.all(patch.landmark_labels[rr, cc] == 0)
def test_add_region(self, patch_data_zeros):
"""
Test adding a region
Args:
patch_data_zeros: Image data containing all zeros
Test Condition:
The points in the mask at the given position are set to 1
"""
patch = Patch(patch_data_zeros, (4, 4))
patch._mask = patch_data_zeros
position = (5, 5)
radius = 3
patch.add_region(position, radius)
rr, cc = patch._get_circle(position, radius)
assert np.all(patch.mask[rr, cc] == 1)
def test_add_landmark(self, patch_data_ones):
"""
Test adding a landmark
Args:
patch_data_ones: Image data containing all ones
Test Condition:
The points in the landmark labels matrix at the given position are
equal to the label given to them
"""
patch = Patch(patch_data_ones, (4, 4))
patch._mask = patch_data_ones
position = (5, 5)
radius = 3
label = 7
patch.add_landmark(position, radius, label)
rr, cc = patch._get_circle(position, radius)
assert np.all(patch.landmark_labels[rr, cc] == 7)