def test_align3d_4():
"""
Test alignment.
"""
dx = numpy.array([0.1, 0.15, -0.08])
#dx = numpy.array([0.1, 0.01, 0.001])
image1 = dg.drawGaussiansXYZ((12,13,14),
numpy.array([6.0]),
numpy.array([6.5]),
numpy.array([7.0]))
# a3d = imgCorr.Align3DProductLM(image1, xy_margin = 1, z_margin = 1)
a3d = imgCorr.Align3DProductNewtonCG(image1, xy_margin = 1, z_margin = 1)
image2 = dg.drawGaussiansXYZ((12,13,14),
numpy.array([6.0 - dx[0]]),
numpy.array([6.5 - dx[1]]),
numpy.array([7.0 - dx[2]]))
a3d.setOtherImage(image2)
# Check that we find the proper alignment.
[disp, success, fun, status] = a3d.maximize()
assert(success)
assert(numpy.allclose(disp, dx, rtol = 0.01, atol = 0.01))
# Check returning an aligned other.
[aligned, q_score, disp] = a3d.align()
assert(q_score > 10.0)
assert(numpy.allclose(image1, aligned, rtol = 1.0e-2, atol = 1.0e-2))
def test_align3d_4():
"""
Test alignment.
"""
dx = numpy.array([0.1, 0.15, -0.08])
#dx = numpy.array([0.1, 0.01, 0.001])
image1 = dg.drawGaussiansXYZ((12, 13, 14), numpy.array([6.0]),
numpy.array([6.5]), numpy.array([7.0]))
# a3d = imgCorr.Align3DProductLM(image1, xy_margin = 1, z_margin = 1)
a3d = imgCorr.Align3DProductNewtonCG(image1, xy_margin=1, z_margin=1)
image2 = dg.drawGaussiansXYZ((12, 13, 14), numpy.array([6.0 - dx[0]]),
numpy.array([6.5 - dx[1]]),
numpy.array([7.0 - dx[2]]))
a3d.setOtherImage(image2)
# Check that we find the proper alignment.
[disp, success, fun, status] = a3d.maximize()
assert (success)
assert (numpy.allclose(disp, dx, rtol=0.01, atol=0.01))
# Check returning an aligned other.
[aligned, q_score, disp] = a3d.align()
assert (q_score > 10.0)
assert (numpy.allclose(image1, aligned, rtol=1.0e-2, atol=1.0e-2))
def test_align3d_2():
"""
Test displacement
"""
image1 = dg.drawGaussiansXYZ((12, 13, 14), numpy.array([6.0]),
numpy.array([6.5]), numpy.array([7.0]))
a3d = imgCorr.Align3DProduct(image1, xy_margin=1, z_margin=1)
a3d.setOtherImage(image1)
val = a3d.func(numpy.zeros(3))
image2 = dg.drawGaussiansXYZ((12, 13, 14), numpy.array([6.1]),
numpy.array([6.6]), numpy.array([6.9]))
a3d.setOtherImage(image2)
assert (a3d.func(numpy.array([0.0, 0.0, 0.0])) < (val - 0.01))
assert (a3d.func(numpy.array([0.1, 0.1, -0.1])) < (val - 0.01))
assert (abs(a3d.func(numpy.array([-0.1, -0.1, 0.1])) - val) < 1.0e-4)
def test_dgxy_2():
image = dg.drawGaussiansXYZ((20, 20, 20), numpy.array([10.0]),
numpy.array([10.0]), numpy.array([10.0]))
dx = numpy.arange(-10.0, 10, 1.0)
g_slice = numpy.exp(-dx * dx / 2.0)
assert (numpy.allclose(g_slice, image[10, 10, :], atol=1.0e-4))
assert (numpy.allclose(g_slice, image[10, :, 10], atol=1.0e-4))
assert (numpy.allclose(g_slice, image[:, 10, 10], atol=1.0e-4))
def test_dgxy_2():
image = dg.drawGaussiansXYZ((20,20,20),
numpy.array([10.0]),
numpy.array([10.0]),
numpy.array([10.0]))
dx = numpy.arange(-10.0,10,1.0)
g_slice = numpy.exp(-dx*dx/2.0)
assert(numpy.allclose(g_slice, image[10,10,:], atol = 1.0e-4))
assert(numpy.allclose(g_slice, image[10,:,10], atol = 1.0e-4))
assert(numpy.allclose(g_slice, image[:,10,10], atol = 1.0e-4))
def test_align3d_2():
"""
Test displacement
"""
image1 = dg.drawGaussiansXYZ((12,13,14),
numpy.array([6.0]),
numpy.array([6.5]),
numpy.array([7.0]))
a3d = imgCorr.Align3DProduct(image1, xy_margin = 1, z_margin = 1)
a3d.setOtherImage(image1)
val = a3d.func(numpy.zeros(3))
image2 = dg.drawGaussiansXYZ((12,13,14),
numpy.array([6.1]),
numpy.array([6.6]),
numpy.array([6.9]))
a3d.setOtherImage(image2)
assert(a3d.func(numpy.array([0.0, 0.0, 0.0])) < (val - 0.01))
assert(a3d.func(numpy.array([0.1, 0.1, -0.1])) < (val - 0.01))
assert(abs(a3d.func(numpy.array([-0.1, -0.1, 0.1])) - val) < 1.0e-4)
def test_dgxy_2():
image = dg.drawGaussiansXYZ((20,20,20),
numpy.array([10.0]),
numpy.array([10.0]),
numpy.array([10.0]))
dx = numpy.arange(-10.0,10,1.0)
g_slice = numpy.exp(-dx*dx/2.0)
if True:
with tifffile.TiffWriter("dg.tif") as tf:
for i in range(image.shape[0]):
tf.save(image[i,:,:].astype(numpy.float32))
assert(numpy.allclose(g_slice, image[10,10,:], atol = 1.0e-4))
assert(numpy.allclose(g_slice, image[10,:,10], atol = 1.0e-4))
assert(numpy.allclose(g_slice, image[:,10,10], atol = 1.0e-4))
def test_align_psfs_1():
"""
Test alignment of multiple PSFs to each other.
"""
pos = [5.0, 6.0, 7.0]
maxd = 3.0
psfs = []
for i in range(7):
psfs.append(
dg.drawGaussiansXYZ((12, 13, 14),
numpy.array([pos[0] + int(i / maxd)]),
numpy.array([pos[1] + int(i / maxd)]),
numpy.array([pos[2] + int(i / maxd)])))
[average_psf, i_score] = mPSFUtils.alignPSFs(psfs)
assert (i_score > 2.1)
if False:
with tifffile.TiffWriter("psf.tif") as tf:
tf.save(mPSFUtils.averagePSF(psfs)[6, :, :].astype(numpy.float32))
tf.save(average_psf[6, :, :].astype(numpy.float32))
def test_align3d_3():
"""
Test on Gaussians.
"""
image = dg.drawGaussiansXYZ((12,13,14),
numpy.array([6.0]),
numpy.array([6.5]),
numpy.array([7.0]))
a3d = imgCorr.Align3DProduct(image, xy_margin = 1, z_margin = 1)
a3d.setOtherImage(image)
# Check X derivatives.
for elt in [-0.1, 0.0, 0.1]:
dx = 1.0e-6
f1 = a3d.func(numpy.array([elt + dx, 0.0, 0.0]))
f2 = a3d.func(numpy.array([elt, 0.0, 0.0]))
est = (f1-f2)/dx
exact = a3d.jacobian(numpy.array([elt, 0.0, 0.0]))[0]
assert(abs(est - exact) < 1.0e-3)
# Check Y derivatives.
for elt in [-0.1, 0.0, 0.1]:
dx = 1.0e-6
f1 = a3d.func(numpy.array([0.0, elt + dx, 0.0]))
f2 = a3d.func(numpy.array([0.0, elt, 0.0]))
est = (f1-f2)/dx
exact = a3d.jacobian(numpy.array([0.0, elt, 0.0]))[1]
assert(abs(est - exact) < 1.0e-3)
# Check Z derivatives.
for elt in [-0.1, 0.0, 0.1]:
dx = 1.0e-6
f1 = a3d.func(numpy.array([0.0, 0.0, elt + dx]))
f2 = a3d.func(numpy.array([0.0, 0.0, elt]))
est = (f1-f2)/dx
exact = a3d.jacobian(numpy.array([0.0, 0.0, elt]))[2]
assert(abs(est - exact) < 1.0e-3)
def test_align3d_3():
"""
Test on Gaussians.
"""
image = dg.drawGaussiansXYZ((12, 13, 14), numpy.array([6.0]),
numpy.array([6.5]), numpy.array([7.0]))
a3d = imgCorr.Align3DProduct(image, xy_margin=1, z_margin=1)
a3d.setOtherImage(image)
# Check X derivatives.
for elt in [-0.1, 0.0, 0.1]:
dx = 1.0e-6
f1 = a3d.func(numpy.array([elt + dx, 0.0, 0.0]))
f2 = a3d.func(numpy.array([elt, 0.0, 0.0]))
est = (f1 - f2) / dx
exact = a3d.jacobian(numpy.array([elt, 0.0, 0.0]))[0]
assert (abs(est - exact) < 1.0e-3)
# Check Y derivatives.
for elt in [-0.1, 0.0, 0.1]:
dx = 1.0e-6
f1 = a3d.func(numpy.array([0.0, elt + dx, 0.0]))
f2 = a3d.func(numpy.array([0.0, elt, 0.0]))
est = (f1 - f2) / dx
exact = a3d.jacobian(numpy.array([0.0, elt, 0.0]))[1]
assert (abs(est - exact) < 1.0e-3)
# Check Z derivatives.
for elt in [-0.1, 0.0, 0.1]:
dx = 1.0e-6
f1 = a3d.func(numpy.array([0.0, 0.0, elt + dx]))
f2 = a3d.func(numpy.array([0.0, 0.0, elt]))
est = (f1 - f2) / dx
exact = a3d.jacobian(numpy.array([0.0, 0.0, elt]))[2]
assert (abs(est - exact) < 1.0e-3)