def test_mass(self):
# The mass calculated from the processed image should be independent
# of added noise. Its absolute value is untested.
# The mass calculated from the raw image should equal
# noiseless mass + noise_size/2 * Npx_in_mask.
self.check_skip()
ndim = 2
radius = 6
N = 20
shape = (128, 127)
# Calculate the expected mass from a single spot using the set masksize
center = (radius * 2, ) * ndim
spot = draw_spots((radius * 4, ) * ndim, [center],
radius * 3,
bitdepth=12)
rect = [slice(c - radius, c + radius + 1) for c in center]
mask = tp.masks.binary_mask(radius, 2)
Npx = mask.sum()
EXPECTED_MASS = (spot[rect] * mask).sum()
# Generate feature locations and make the image
expected = gen_nonoverlapping_locations(shape, N, radius * 3,
radius + 2)
expected = expected + np.random.random(expected.shape)
N = expected.shape[0]
image = draw_spots(shape, expected, radius * 3, bitdepth=12)
# analyze the image without noise
f = tp.locate(image, radius * 2 + 1, engine=self.engine, topn=N)
PROCESSED_MASS = f['mass'].mean()
assert_allclose(f['raw_mass'].mean(), EXPECTED_MASS, rtol=0.01)
for n, noise in enumerate(np.arange(0.05, 0.8, 0.05)):
noise_level = int((2**12 - 1) * noise)
image_noisy = image + np.array(np.random.randint(
0, noise_level, image.shape),
dtype=image.dtype)
f = tp.locate(image_noisy,
radius * 2 + 1,
engine=self.engine,
topn=N)
assert_allclose(f['mass'].mean(), PROCESSED_MASS, rtol=0.1)
assert_allclose(f['raw_mass'].mean(),
EXPECTED_MASS + Npx * noise_level / 2,
rtol=0.1)
def test_oldmass_16bit(self):
old_minmass = 2800000
im = draw_spots(self.shape, self.pos, self.size, bitdepth=16,
noise_level=10000)
new_minmass = self.minmass_v02_to_v04(im, old_minmass)
f = tp.locate(im, self.tp_diameter, minmass=new_minmass)
assert len(f) == self.N
def test_nocharacterize_a(self):
pos = gen_nonoverlapping_locations((200, 300), 9, 5)
image = draw_spots((200, 300), pos, (0.5, 1))
f_c = tp.locate(image, (3, 5), engine=self.engine, characterize=True)
f_nc = tp.locate(image, (3, 5), engine=self.engine, characterize=False)
assert len(f_nc.columns) == 3
assert_allclose(f_c.values[:, :3], f_nc.values)
def test_nocharacterize(self):
pos = gen_nonoverlapping_locations((200, 300), 9, 5)
image = draw_spots((200, 300), pos, 5)
f_c = tp.locate(image, 5, engine=self.engine, characterize=True)
f_nc = tp.locate(image, 5, engine=self.engine, characterize=False)
assert len(f_nc.columns) == 3
assert_allclose(f_c.values[:, :3], f_nc.values)
def test_oldmass_float(self):
old_minmass = 5500
im = draw_spots(self.shape, self.pos, self.size, bitdepth=8,
noise_level=50)
im = (im / im.max()).astype(np.float)
new_minmass = self.minmass_v02_to_v04(im, old_minmass)
f = tp.locate(im, self.tp_diameter, minmass=new_minmass)
assert len(f) == self.N
def test_oldmass_16bit(self):
old_minmass = 2800000
im = draw_spots(self.shape, self.pos, self.draw_diameter, bitdepth=16,
noise_level=10000)
new_minmass = tp.minmass_version_change(im, old_minmass,
smoothing_size=self.tp_diameter)
f = tp.locate(im, self.tp_diameter, minmass=new_minmass)
assert len(f) == self.N
def test_oldmass_float(self):
old_minmass = 5500
im = draw_spots(self.shape, self.pos, self.draw_diameter, bitdepth=8,
noise_level=50)
im = (im / im.max()).astype(np.float)
new_minmass = tp.minmass_version_change(im, old_minmass,
smoothing_size=self.tp_diameter)
f = tp.locate(im, self.tp_diameter, minmass=new_minmass)
assert len(f) == self.N
def test_oldmass_invert(self):
old_minmass = 2800000
im = draw_spots(self.shape, self.pos, self.draw_diameter, bitdepth=12,
noise_level=500)
im = (im.max() - im + 10000)
new_minmass = tp.minmass_version_change(im, old_minmass, invert=True,
smoothing_size=self.tp_diameter)
f = tp.locate(im, self.tp_diameter, minmass=new_minmass, invert=True)
assert len(f) == self.N
def test_oldmass_invert(self):
old_minmass = 2800000
im = draw_spots(self.shape, self.pos, self.size, bitdepth=12,
noise_level=500)
im = (im.max() - im + 10000)
new_minmass = self.minmass_v02_to_v04(im, old_minmass, invert=True)
f = tp.locate(invert_image(im), self.tp_diameter, minmass=new_minmass)
assert len(f) == self.N
def test_mass(self):
# The mass calculated from the processed image should be independent
# of added noise. Its absolute value is untested.
# The mass calculated from the raw image should equal
# noiseless mass + noise_size/2 * Npx_in_mask.
self.check_skip()
ndim = 2
size = 3 # for drawing
radius = 6 # for locate
diameter = radius * 2 + 1
N = 20
shape = (128, 127)
# Calculate the expected mass from a single spot using the set masksize
center = (diameter,) * ndim
spot = draw_spots((diameter*2,) * ndim, [center], size, bitdepth=12)
rect = [slice(c - radius, c + radius + 1) for c in center]
mask = tp.masks.binary_mask(radius, 2)
Npx = mask.sum()
EXPECTED_MASS = (spot[rect] * mask).sum()
# Generate feature locations and make the image
expected = gen_nonoverlapping_locations(shape, N, diameter, diameter)
expected = expected + np.random.random(expected.shape)
N = expected.shape[0]
image = draw_spots(shape, expected, size, bitdepth=12)
# analyze the image without noise
f = tp.locate(image, diameter, engine=self.engine, topn=N)
PROCESSED_MASS = f['mass'].mean()
assert_allclose(f['raw_mass'].mean(), EXPECTED_MASS, rtol=0.01)
for n, noise in enumerate(np.arange(0.05, 0.8, 0.05)):
noise_level = int((2**12 - 1) * noise)
image_noisy = image + np.array(np.random.randint(0, noise_level,
image.shape),
dtype=image.dtype)
f = tp.locate(image_noisy, radius*2+1, engine=self.engine, topn=N)
assert_allclose(f['mass'].mean(), PROCESSED_MASS, rtol=0.1)
assert_allclose(f['raw_mass'].mean(),
EXPECTED_MASS + Npx*noise_level/2, rtol=0.1)
def test_oldmass_16bit(self):
old_minmass = 2800000
im = draw_spots(self.shape,
self.pos,
self.size,
bitdepth=16,
noise_level=10000)
new_minmass = self.minmass_v02_to_v04(im, old_minmass)
f = tp.locate(im, self.tp_diameter, minmass=new_minmass)
assert len(f) == self.N
def test_oldmass_float(self):
old_minmass = 5500
im = draw_spots(self.shape,
self.pos,
self.size,
bitdepth=8,
noise_level=50)
im = (im / im.max()).astype(float)
new_minmass = self.minmass_v02_to_v04(im, old_minmass)
f = tp.locate(im, self.tp_diameter, minmass=new_minmass)
assert len(f) == self.N
def test_oldmass_invert(self):
old_minmass = 2800000
im = draw_spots(self.shape,
self.pos,
self.size,
bitdepth=12,
noise_level=500)
im = (im.max() - im + 10000)
new_minmass = self.minmass_v02_to_v04(im, old_minmass, invert=True)
f = tp.locate(invert_image(im), self.tp_diameter, minmass=new_minmass)
assert len(f) == self.N
def compare(shape, count, radius, noise_level, engine):
radius = tp.utils.validate_tuple(radius, len(shape))
# tp.locate ignores a margin of size radius, take 1 px more to be safe
margin = tuple([r + 1 for r in radius])
diameter = tuple([(r * 2) + 1 for r in radius])
draw_range = tuple([d * 3 for d in diameter])
cols = ['x', 'y', 'z'][:len(shape)][::-1]
pos = gen_nonoverlapping_locations(shape, count, draw_range, margin)
image = draw_spots(shape, pos, draw_range, noise_level)
f = tp.locate(image, diameter, engine=engine)
actual = f[cols].sort(cols)
expected = DataFrame(pos, columns=cols).sort(cols)
return actual, expected
def test_ep(self):
# Test whether the estimated static error equals the rms deviation from
# the expected values. Next to the feature mass, the static error is
# calculated from the estimated image background level and variance.
# This estimate is also tested here.
# A threshold is necessary to identify the background array so that
# background average and standard deviation can be estimated within 1%
# accuracy.
# The (absolute) tolerance for ep in this test is 0.05 pixels.
# Parameters are tweaked so that there is no deviation due to a too
# small mask size. Signal/noise ratios up to 50% are tested.
self.check_skip()
draw_diameter = 21
locate_diameter = 15
N = 200
shape = (512, 513)
noise_expectation = np.array([1 / 2.,
np.sqrt(1 / 12.)]) # average, stdev
# Generate feature locations and make the image
expected = gen_nonoverlapping_locations(shape, N, draw_diameter,
locate_diameter)
expected = expected + np.random.random(expected.shape)
N = expected.shape[0]
image = draw_spots(shape, expected, draw_diameter, bitdepth=12)
for n, noise in enumerate([0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5]):
noise_level = int((2**12 - 1) * noise)
image_noisy = image + np.array(np.random.randint(
0, noise_level, image.shape),
dtype=image.dtype)
f = tp.locate(image_noisy,
locate_diameter,
engine=self.engine,
topn=N,
threshold=noise_level / 4)
_, actual = sort_positions(f[['y', 'x']].values, expected)
rms_dev = np.sqrt(np.mean(np.sum((actual - expected)**2, 1)))
assert_allclose(rms_dev, f['ep'].mean(), atol=0.05)
# Additionally test the measured noise
actual_noise = tp.uncertainty.measure_noise(
image, image_noisy, locate_diameter // 2)
assert_allclose(actual_noise,
noise_expectation * noise_level,
rtol=0.01,
atol=1)
def compare(shape, count, radius, noise_level, **kwargs):
radius = tp.utils.validate_tuple(radius, len(shape))
# tp.locate ignores a margin of size radius, take 1 px more to be safe
margin = tuple([r + 1 for r in radius])
diameter = tuple([(r * 2) + 1 for r in radius])
size = [d / 2 for d in diameter]
separation = tuple([d * 3 for d in diameter])
cols = ['x', 'y', 'z'][:len(shape)][::-1]
pos = gen_nonoverlapping_locations(shape, count, separation, margin)
image = draw_spots(shape, pos, size, noise_level)
f = tp.locate(image, diameter, **kwargs)
actual = pandas_sort(f[cols], cols)
expected = pandas_sort(DataFrame(pos, columns=cols), cols)
return actual, expected
def compare(shape, count, radius, noise_level, **kwargs):
radius = tp.utils.validate_tuple(radius, len(shape))
# tp.locate ignores a margin of size radius, take 1 px more to be safe
margin = tuple([r + 1 for r in radius])
diameter = tuple([(r * 2) + 1 for r in radius])
size = [d / 2 for d in diameter]
separation = tuple([d * 3 for d in diameter])
cols = ['x', 'y', 'z'][:len(shape)][::-1]
pos = gen_nonoverlapping_locations(shape, count, separation, margin)
image = draw_spots(shape, pos, size, noise_level)
f = tp.locate(image, diameter, **kwargs)
actual = pandas_sort(f[cols], cols)
expected = pandas_sort(DataFrame(pos, columns=cols), cols)
return actual, expected
def test_ep(self):
# Test wether the estimated static error equals the rms deviation from
# the expected values. Next to the feature mass, the static error is
# calculated from the estimated image background level and variance.
# This estimate is also tested here.
# A threshold is necessary to identify the background array so that
# background average and standard deviation can be estimated within 1%
# accuracy.
# The (absolute) tolerance for ep in this test is 0.05 pixels.
# Parameters are tweaked so that there is no deviation due to a too
# small mask size. Signal/noise ratios upto 50% are tested.
self.check_skip()
draw_diameter = 21
locate_diameter = 15
N = 200
shape = (512, 513)
noise_expectation = np.array([1/2., np.sqrt(1/12.)]) # average, stdev
# Generate feature locations and make the image
expected = gen_nonoverlapping_locations(shape, N, draw_diameter,
locate_diameter)
expected = expected + np.random.random(expected.shape)
N = expected.shape[0]
image = draw_spots(shape, expected, draw_diameter, bitdepth=12)
for n, noise in enumerate([0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5]):
noise_level = int((2**12 - 1) * noise)
image_noisy = image + np.array(np.random.randint(0, noise_level,
image.shape),
dtype=image.dtype)
f = tp.locate(image_noisy, locate_diameter, engine=self.engine,
topn=N, threshold=noise_level/4)
_, actual = sort_positions(f[['y', 'x']].values, expected)
rms_dev = np.sqrt(np.mean(np.sum((actual-expected)**2, 1)))
assert_allclose(rms_dev, f['ep'].mean(), atol=0.05)
# Additionally test the measured noise
actual_noise = tp.uncertainty.measure_noise(image_noisy,
locate_diameter,
noise_level/4)
assert_allclose(actual_noise, noise_expectation * noise_level,
rtol=0.01, atol=1)
def setUp(self):
pos = gen_nonoverlapping_locations((512, 512), 200, 20)
self.frame = draw_spots((512, 512), pos, 20, noise_level=100)
self.margin = 11
self.bp_scipy = bandpass(self.frame, 2, 11)[self.margin:-self.margin,
self.margin:-self.margin]
from __future__ import division
import nose
from numpy.testing.utils import assert_allclose
from trackpy.preprocessing import (bandpass, legacy_bandpass,
legacy_bandpass_fftw)
from trackpy.artificial import gen_nonoverlapping_locations, draw_spots
from trackpy.tests.common import StrictTestCase
pos = gen_nonoverlapping_locations((512, 512), 200, 20)
frame = draw_spots((512, 512), pos, 20, noise_level=100)
margin = 11
bp_scipy = bandpass(frame, 3, 11)[margin:-margin, margin:-margin]
def test_legacy_bandpass():
lbp_numpy = legacy_bandpass(frame, 3, 11)[margin:-margin, margin:-margin]
assert_allclose(lbp_numpy, bp_scipy, atol=1.1)
def test_legacy_bandpass_fftw():
try:
import pyfftw
except ImportError:
raise nose.SkipTest("pyfftw not installed. Skipping.")
lbp_fftw = legacy_bandpass_fftw(frame, 3, 11)[margin:-margin, margin:-margin]
assert_allclose(lbp_fftw, bp_scipy, atol=1.1)
if __name__ == '__main__':
import nose
nose.runmodule(argv=[__file__, '-vvs', '-x', '--pdb', '--pdb-failure'],
from __future__ import division
import nose
from numpy.testing.utils import assert_allclose
from trackpy.preprocessing import *
from trackpy.artificial import gen_nonoverlapping_locations, draw_spots
pos = gen_nonoverlapping_locations((512, 512), 200, 20)
frame = draw_spots((512, 512), pos, 20, noise_level=100)
margin = 11
bp_scipy = bandpass(frame, 3, 11)[margin:-margin, margin:-margin]
def test_legacy_bandpass():
lbp_numpy = legacy_bandpass(frame, 3, 11)[margin:-margin, margin:-margin]
assert_allclose(lbp_numpy, bp_scipy, atol=1.1)
def test_legacy_bandpass_fftw():
try:
import pyfftw
except ImportError:
raise nose.SkipTest("pyfftw not installed. Skipping.")
lbp_fftw = legacy_bandpass_fftw(frame, 3, 11)[margin:-margin,
margin:-margin]
assert_allclose(lbp_fftw, bp_scipy, atol=1.1)
if __name__ == '__main__':
import nose
nose.runmodule(argv=[__file__, '-vvs', '-x', '--pdb', '--pdb-failure'],
exit=False)