def test_orientation():
"""counter-clockwise vs clockwise"""
# Helper definitions to get an ellipse
major = 10
minor = 5
ellip = get_ellipse_coords(a=major,
b=minor,
x=minor,
y=5,
angle=0,
k=100)
# obtain the centroid (corresponds to pos_x and pos_lat)
cx, cy = centroid_of_polygon(ellip)
v1 = get_volume(cont=ellip,
pos_x=cx,
pos_y=cy,
pix=1)
# Turn contour around
v2 = get_volume(cont=ellip[::-1, :],
pos_x=cx,
pos_y=cy,
pix=1)
assert np.all(v1 == v2)
def test_volume():
ds = new_dataset(retrieve_data("rtdc_data_hdf5_mask_contour.zip"))
mask = [mi for mi in ds["mask"]]
cont1 = [ci for ci in ds["contour"]]
cont2 = get_contour(mask)
kw = dict(pos_x=ds["pos_x"],
pos_y=ds["pos_y"],
pix=ds.config["imaging"]["pixel size"])
v1 = get_volume(cont=cont1, **kw)
v2 = get_volume(cont=cont2, **kw)
assert np.allclose(v1, v2)
cleanup()
def features_from_mask(mask, pixel_size=0.34):
"""Compute dclab features from a binary mask image
This essentially mimicks what Shape-In does with OpenCV.
Parameters
----------
mask: 2d boolean ndarray
binary mask image
pixel_size: float
Detector pixel size [um]
"""
cont_raw = get_contour(mask)
# this is how Shape-In does things
cont = cv2.convexHull(cont_raw)
arc = cv2.arcLength(cont, True)
mu = cv2.moments(cont, False)
pos_x = (mu["m10"] / mu["m00"]) * pixel_size
pos_y = (mu["m01"] / mu["m00"]) * pixel_size
feats = {
# scalar features
"area_um": mu["m00"] * pixel_size**2,
"deform": 1 - 2.0 * np.sqrt(np.pi * mu["m00"]) / arc,
"inert_ratio_cvx": np.sqrt(mu["mu20"] / mu["mu02"]),
"pos_x": pos_x,
"pos_y": pos_y,
"volume": get_volume(cont_raw, pos_x, pos_y, pixel_size),
# image data
"image": np.array(254 * mask, dtype=np.uint8),
"mask": mask,
}
return feats
def test_xpos():
"""xpos is not necessary to compute volume dense ellipse"""
major = 10
minor = 5
ellip = get_ellipse_coords(a=major,
b=minor,
x=minor,
y=5.0,
angle=0,
k=100)
cx, cy = centroid_of_polygon(ellip)
# no lists
v0 = get_volume(cont=ellip, pos_x=cx, pos_y=cy, pix=1)
for cxi in np.linspace(0, 2 * cx, 10):
vi = get_volume(cont=ellip, pos_x=cxi, pos_y=cy, pix=1)
assert np.allclose(v0, vi)
def test_shape():
major = 10
minor = 5
ellip = get_ellipse_coords(a=major,
b=minor,
x=minor,
y=5.0,
angle=0,
k=100)
cx, cy = centroid_of_polygon(ellip)
# no lists
volume = get_volume(cont=ellip, pos_x=cx, pos_y=cy, pix=1)
assert isinstance(volume, float)
volumelist = get_volume(cont=[ellip], pos_x=[cx], pos_y=[cy], pix=1)
assert isinstance(volumelist, np.ndarray)
def test_xpos():
"""xpos is not necessary to compute volume dense ellipse"""
major = 10
minor = 5
ellip = get_ellipse_coords(a=major,
b=minor,
x=minor,
y=5.0,
angle=0,
k=100)
cx, cy = centroid_of_polygon(ellip)
# no lists
v0 = get_volume(cont=ellip,
pos_x=cx,
pos_y=cy,
pix=1)
for cxi in np.linspace(0, 2 * cx, 10):
vi = get_volume(cont=ellip,
pos_x=cxi,
pos_y=cy,
pix=1)
assert np.allclose(v0, vi)
def test_shape():
major = 10
minor = 5
ellip = get_ellipse_coords(a=major,
b=minor,
x=minor,
y=5.0,
angle=0,
k=100)
cx, cy = centroid_of_polygon(ellip)
# no lists
volume = get_volume(cont=ellip,
pos_x=cx,
pos_y=cy,
pix=1)
assert isinstance(volume, float)
volumelist = get_volume(cont=[ellip],
pos_x=[cx],
pos_y=[cy],
pix=1)
assert isinstance(volumelist, np.ndarray)
def test_orientation():
"""counter-clockwise vs clockwise"""
# Helper definitions to get an ellipse
major = 10
minor = 5
ellip = get_ellipse_coords(a=major, b=minor, x=minor, y=5, angle=0, k=100)
# obtain the centroid (corresponds to pos_x and pos_lat)
cx, cy = centroid_of_polygon(ellip)
v1 = get_volume(cont=ellip,
pos_x=cx,
pos_y=cy,
pix=1,
fix_orientation=True)
# Turn contour around
v2 = get_volume(cont=ellip[::-1, :],
pos_x=cx,
pos_y=cy,
pix=1,
fix_orientation=True)
assert np.all(v1 == v2)
def test_get_volume():
# Helper definitions to get an ellipse
major = 10
minor = 5
ellip = get_ellipse_coords(a=major, b=minor, x=minor, y=5, angle=0, k=100)
# obtain the centroid (corresponds to pos_x and pos_lat)
cx, cy = centroid_of_polygon(ellip)
volume = get_volume(cont=[ellip],
pos_x=[cx],
pos_y=[cy],
pix=1,
fix_orientation=True)
# Analytic solution for volume of ellipsoid:
v = 4 / 3 * np.pi * major * minor**2
msg = "Calculation of volume is faulty!"
assert np.allclose(np.array(volume), np.array(v)), msg
def test_get_volume():
# Helper definitions to get an ellipse
major = 10
minor = 5
ellip = get_ellipse_coords(a=major,
b=minor,
x=minor,
y=5,
angle=0,
k=100)
# obtain the centroid (corresponds to pos_x and pos_lat)
cx, cy = centroid_of_polygon(ellip)
elliplist = []
elliplist.append(ellip)
volume = get_volume(cont=elliplist,
pos_x=[cx],
pos_y=[cy],
pix=1)
# Analytic solution for volume of ellipsoid:
V = 4 / 3 * np.pi * major * minor**2
msg = "Calculation of volume is faulty!"
assert np.allclose(np.array(volume), np.array(V)), msg