def test_transform(self):
roi = ROI.ROI(polygons=[[0, 0], [0, 2], [2, 2], [2, 0]],
im_shape=(3, 3))
transforms = [np.array([[1, 0, 0], [0, 1, 0]])] # one per plane
roi_list = ROI.ROIList([roi])
assert_equal(roi_list.transform(transforms)[0].coords, roi.coords)
def test_postprocess(self):
centers = [(10, 10), (40, 40), (70, 70), (100, 100)]
roi_xy = [
np.arange(self.tiff_ds.sequences[0].shape[2]),
np.arange(self.tiff_ds.sequences[0].shape[3])
]
rois = ROI.ROIList([
ROI.ROI(_gaussian_2d(roi_xy, center, (10, 10)))
for center in centers
])
tobool = segment.SparseROIsFromMasks(n_processes=2)
smooth = segment.SmoothROIBoundaries(n_processes=2)
rois = smooth.apply(tobool.apply(rois))
assert_(len(rois) == len(centers))
for roi in rois:
polygon = mplPath.Path(roi.coords[0][:, :2])
for nc, center in enumerate(centers):
if polygon.contains_point(center):
centers.pop(nc)
break
assert_(len(centers) == 0)
def test_poly2mask():
poly1 = [[0, 0], [0, 1], [1, 1], [1, 0]]
poly2 = [[0, 1], [0, 2], [2, 2], [2, 1]]
masks = ROI.poly2mask([poly1, poly2], (3, 3))
assert_equal(
masks[0].todense(),
np.matrix([[True, False, False],
[True, True, False],
[False, False, False]], dtype=bool))
def test_mask2poly():
mask = np.zeros((10, 10), dtype=bool)
mask[2:4, 3:7] = True
multi_poly = ROI.mask2poly(mask)
assert_equal(
np.array(multi_poly[0].exterior.coords),
np.array([[7., 3.5, 0.], [7., 2.5, 0.], [6.5, 2., 0.], [3.5, 2., 0.],
[3., 2.5, 0.], [3., 3.5, 0.], [3.5, 4., 0.], [6.5, 4., 0.],
[7., 3.5, 0.]]))
def test_poly2mask():
poly1 = [[0, 0], [0, 1], [1, 1], [1, 0]]
poly2 = [[0, 1], [0, 2], [2, 2], [2, 1]]
masks = ROI.poly2mask([poly1, poly2], (3, 3))
assert_equal(
masks[0].todense(),
np.matrix(
[[True, False, False], [True, True, False], [False, False, False]],
dtype=bool))
def test_ROI(self):
roi = ROI.ROI(polygons=[[0, 0], [0, 1], [1, 1], [1, 0]],
im_shape=(2, 2))
assert_equal(roi.coords, [
np.array([[0., 0., 0.], [0., 1., 0.], [1., 1., 0.], [1., 0., 0.],
[0., 0., 0.]])
])
assert_equal(roi.mask[0].todense(),
np.matrix([[True, False], [False, False]], dtype=bool))
def test_mask2poly():
mask = np.zeros((10, 10), dtype=bool)
mask[2:4, 3:7] = True
multi_poly = ROI.mask2poly(mask)
assert_equal(
np.array(multi_poly[0].exterior.coords),
np.array([[7., 3.5, 0.],
[7., 2.5, 0.],
[6.5, 2., 0.],
[3.5, 2., 0.],
[3., 2.5, 0.],
[3., 3.5, 0.],
[3.5, 4., 0.],
[6.5, 4., 0.],
[7., 3.5, 0.]]))
