def test_no_mask(self):
"""roi.PathROI.transform: no_image=True"""
r = roi.PathROI([[1, 1], [2, 2]], buffer=1.5, no_image=True)
roi2 = r.transform()
self.assertIsInstance(roi2, roi.PathROI)
self.assertEqual(r.buffer, roi2.buffer)
self.assertIs(roi2.image_mask, None)
def test_eq(self):
""".__eq__"""
path = self.roi.path
r1 = roi.PathROI(path, buffer=0)
r2 = roi.PathROI(path, buffer=0)
assert r1 == r2
v3 = path.vertices.copy()
v3[1] += 0.5
r3 = roi.PathROI(mpl.path.Path(v3, path.codes), buffer=0)
assert r1 != r3
c4 = path.codes.copy()
c4[1] = 1
r4 = roi.PathROI(mpl.path.Path(path.vertices, c4), buffer=0)
assert r1 != r4
r5 = roi.PathROI(path, buffer=0.5)
assert r1 != r5
def test_init_open(self):
""".__init__: open path"""
r = roi.PathROI(self.vertices[:-1, :], buffer=self.buffer)
np.testing.assert_array_equal(r.path.vertices, self.vertices)
np.testing.assert_allclose(r.bounding_box, self.bbox)
np.testing.assert_allclose(r.bounding_box_int, self.bbox_int)
self.assertEqual(r.buffer, self.buffer)
def test_locate_roi_pathroi(self):
# Test locate_roi specifying the ROI as a PathROI
r = roi.PathROI(self.roi_vertices, no_image=True)
peaks = locate_roi(self.frame, r, rel_origin=False, **self.options)
orig = r(self.orig, rel_origin=False)
np.testing.assert_allclose(peaks,
orig[peaks.columns.tolist()],
rtol=1e-6)
def test_batch_roi(self):
# Test the batch_roi function
peaks = batch_roi([self.frame] * 2,
self.roi_vertices,
rel_origin=False,
**self.options)
r = roi.PathROI(self.roi_vertices, no_image=True)
orig = r(self.batch_orig, rel_origin=False)
np.testing.assert_allclose(peaks,
orig[peaks.columns.tolist()],
rtol=1e-3)
def setUp(self):
super().setUp()
self.vertices = np.array(
[[-30, -30], [-30, 20], [20, 20], [20, -30], [-30, -30]],
dtype=float)
self.bbox = np.array([self.vertices[0], self.vertices[2]])
self.bbox_int = self.bbox.astype(int)
self.mask = np.ones((50, 50), dtype=bool)
self.roi = roi.PathROI(self.vertices)
self.loc = pd.DataFrame([[3, 3], [30, 30], [100, 80]],
columns=["x", "y"])
self.loc_roi = self.loc.drop([1, 2])
self.loc_roi_inv = self.loc.drop(0)
def test_locate_roi_vertices(self):
# Test locate_roi specifying the ROI as a list of vertices
# The ROI is chosen so that nothing goes on at its boundaries since
# there differences between locate_roi and locate + applying a ROI
# later arise
r = roi.PathROI(self.roi_vertices, no_image=True)
peaks = locate_roi(self.frame,
self.roi_vertices,
rel_origin=False,
**self.options)
orig = r(self.orig, rel_origin=False)
np.testing.assert_allclose(peaks,
orig[peaks.columns.tolist()],
rtol=1e-6)
def setUp(self):
super().setUp()
self.vertices = np.array(
[[20, 20], [80, 20], [80, 60], [20, 60], [20, 20]],
dtype=float) + 0.7
self.buffer = 10
self.roi = roi.PathROI(self.vertices, buffer=self.buffer)
self.bbox = np.array(
[self.vertices[0] - self.buffer, self.vertices[2] + self.buffer])
self.bbox_int = np.array([[10, 10], [91, 71]])
self.mask = np.zeros((61, 81), dtype=bool)
self.mask[1:, 1:] = True
self.loc = pd.DataFrame([[3, 3], [12, 12], [30, 30], [100, 80]],
columns=["x", "y"])
self.loc_roi = self.loc.drop([0, 3])
self.loc_roi_inv = self.loc.drop([1, 2])
def setUp(self):
self.vertices = np.array(
[[10, 10], [90, 10], [90, 70], [10, 70], [10, 10]],
dtype=float) + 0.7
self.bbox = np.array([self.vertices[0], self.vertices[2]])
self.bbox_int = np.array([[10, 10], [91, 71]])
self.mask = np.zeros((61, 81), dtype=bool)
self.mask[1:, 1:] = True
self.buffer = 0
self.roi = roi.PathROI(self.vertices)
self.img = np.ones((80, 100))
self.loc = pd.DataFrame([[3, 3], [30, 30], [100, 80]],
columns=["x", "y"])
self.loc_roi = self.loc.drop([0, 2])
self.loc_roi_inv = self.loc.drop(1)
def setUp(self):
super().setUp()
self.vertices = self.vertices[::-1]
self.roi = roi.PathROI(self.vertices, buffer=self.buffer)
def setUp(self):
super().setUp()
self.roi = roi.PathROI(self.vertices, no_image=True)
def setUp(self):
self.roi = roi.PathROI([[0, 0], [1, 0], [1, 1], [0, 1]], buffer=1.5)
