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)