def test_translation(self):
transform = Transform('origin', 'local', translation=[3, 4])
point1 = Point2D([0, 0], 'origin', transform)
point2 = Point2D([0, 0], 'local', transform)
np.testing.assert_almost_equal(point1.get_coord('origin'), [0, 0])
np.testing.assert_almost_equal(point1.get_coord('local'), [-3, -4])
np.testing.assert_almost_equal(point2.get_coord('origin'), [3, 4])
np.testing.assert_almost_equal(point2.get_coord('local'), [0, 0])
np.testing.assert_almost_equal(point1.dist(point2), 5)
def test_90deg_rotation(self):
shape = [20, 10] # [width, height]
angle = np.pi / 2
transform = Transform('origin', 'local', dim=shape, angle=angle)
point1 = Point2D([10, 5], 'origin', transform)
point2 = Point2D([5, 10], 'local', transform)
np.testing.assert_almost_equal(point1.get_coord('origin'), [10, 5])
np.testing.assert_almost_equal(point1.get_coord('local'), [5, 10])
np.testing.assert_almost_equal(point2.get_coord('origin'), [10, 5])
np.testing.assert_almost_equal(point2.get_coord('local'), [5, 10])
np.testing.assert_almost_equal(point1.dist(point2), 0)
def test_missing_transform(self):
"""
get coordinate returns a MissingTransformError when requested a coordinate in a frame for which the transform is unknown
"""
transform = Transform('origin', 'local', translation=[0, 0])
point1 = Point2D([400, 100], 'origin', transform)
self.assertRaises(MissingTransformError, point1.get_coord, 'space')
def detect_tomatoes(self):
"""detect tomatoes based on the truss segment"""
pwd = os.path.join(self.pwd, '05_tomatoes')
if self.truss_crop.sum() == 0:
warnings.warn("Detect tomato: no pixel has been classified as truss!")
return False
if self.save:
img_bg = self.img_rgb_crop
else:
img_bg = self.img_rgb_crop
centers, radii, com = detect_tomato(self.truss_crop,
self.settings['detect_tomato'],
px_per_mm=self.px_per_mm,
img_rgb=img_bg,
save=self.save,
pwd=pwd,
name=self.name)
# convert obtained coordinated to two-dimensional points linked to a coordinate frame
self.radii = radii
self.centers = points_from_coords(centers, self.LOCAL_FRAME_ID, self.transform)
self.com = Point2D(com, self.LOCAL_FRAME_ID, self.transform)
if self.com is None:
return False
else:
return True
def test_transform_forwards_backwards(self):
"""
get coordinate return the original coordinate after translating forwards and backwards
"""
shape = [1000, 400] # [width, height]
translation = [50, -10]
for angle_rad in np.arange(-np.pi, np.pi, 10):
transform = Transform('origin', 'local', shape, angle_rad,
translation)
point1 = Point2D([400, 100], 'origin', transform)
coord1 = point1.get_coord('local')
point2 = Point2D(coord1, 'local', transform)
np.testing.assert_almost_equal(point1.get_coord('origin'),
point2.get_coord('origin'))
def test_345_rotation(self):
shape = [8, 6] # [width, height]
angle = -np.arctan2(3, 4)
transform = Transform('origin', 'local', dim=shape, angle=angle)
point1 = Point2D([4, 3], 'origin', transform)
point2 = Point2D([5, 3.0 / 5.0 * 8], 'local', transform)
np.testing.assert_almost_equal(point1.get_coord('origin'), [4, 3])
np.testing.assert_almost_equal(point1.get_coord('local'),
[5, 3.0 / 5.0 * 8])
np.testing.assert_almost_equal(point2.get_coord('origin'), [4, 3])
np.testing.assert_almost_equal(point2.get_coord('local'),
[5, 3.0 / 5.0 * 8])
np.testing.assert_almost_equal(point1.dist(point2), 0)
def detect_peduncle(self):
"""Detect the peduncle and junctions"""
pwd = os.path.join(self.pwd, '06_peduncle')
success = True
if self.save:
img_bg = change_brightness(self.get_segmented_image(local=True), 0.85)
else:
img_bg = self.img_rgb_crop
mask, branch_data, junc_coords, end_coords = detect_peduncle(self.peduncle_crop,
self.settings['detect_peduncle'],
px_per_mm=self.px_per_mm,
save=self.save,
bg_img=img_bg,
name=self.name,
pwd=pwd)
# convert to 2D points
peduncle_points = points_from_coords(np.argwhere(mask)[:, (1, 0)], self.LOCAL_FRAME_ID, self.transform)
junction_points = points_from_coords(junc_coords, self.LOCAL_FRAME_ID, self.transform)
end_points = points_from_coords(end_coords, self.LOCAL_FRAME_ID, self.transform)
for branch_type in branch_data:
for i, branch in enumerate(branch_data[branch_type]):
for lbl in ['coords', 'src_node_coord', 'dst_node_coord', 'center_node_coord']:
if lbl == 'coords':
branch_data[branch_type][i][lbl] = points_from_coords(branch[lbl], self.LOCAL_FRAME_ID,
self.transform)
else:
branch_data[branch_type][i][lbl] = Point2D(branch[lbl], self.LOCAL_FRAME_ID, self.transform)
self.junction_points = junction_points
self.end_points = end_points
self.peduncle_points = peduncle_points
self.branch_data = branch_data
return success
def test_missing_transform(self):
"""
get coordinate returns a MissingTransformError when requested a coordinate when no transform was given
"""
point1 = Point2D([400, 100], 'origin')
self.assertRaises(MissingTransformError, point1.get_coord, 'local')