def test_06_NaN(self):
"""Regression test of Otsu with NaN in input (issue #624)"""
r = np.random.RandomState()
r.seed(6)
data = r.uniform(size=100)
data[r.uniform(size=100) > 0.8] = np.NaN
self.assertEqual(otsu(data), otsu(data[~np.isnan(data)]))
self.assertEqual(entropy(data), entropy(data[~np.isnan(data)]))
self.assertEqual(otsu3(data), otsu3(data[~np.isnan(data)]))
self.assertEqual(entropy3(data), entropy3(data[~np.isnan(data)]))
def test_06_NaN(self):
"""Regression test of Otsu with NaN in input (issue #624)"""
r = np.random.RandomState()
r.seed(6)
data = r.uniform(size=100)
data[r.uniform(size=100) > .8] = np.NaN
self.assertEqual(otsu(data), otsu(data[~np.isnan(data)]))
self.assertEqual(entropy(data), entropy(data[~np.isnan(data)]))
self.assertEqual(otsu3(data), otsu3(data[~np.isnan(data)]))
self.assertEqual(entropy3(data), entropy3(data[~np.isnan(data)]))
def get_otsu_threshold(image,
mask=None,
two_class_otsu=True,
use_weighted_variance=True,
assign_middle_to_foreground=True):
if not mask is None:
image = image[mask]
else:
image = np.array(image.flat)
image = image[image >= 0]
if len(image) == 0:
return 1
image, d = log_transform(image)
if two_class_otsu:
if use_weighted_variance:
threshold = otsu(image)
else:
threshold = entropy(image)
else:
if use_weighted_variance:
t1, t2 = otsu3(image)
else:
t1, t2 = entropy3(image)
threshold = t1 if assign_middle_to_foreground else t2
threshold = inverse_log_transform(threshold, d)
return threshold
def get_otsu_threshold(image, mask = None,
two_class_otsu = True,
use_weighted_variance = True,
assign_middle_to_foreground = True):
if not mask is None:
image = image[mask]
else:
image = np.array(image.flat)
image = image[image >= 0]
if len(image) == 0:
return 1
image, d = log_transform(image)
if two_class_otsu:
if use_weighted_variance:
threshold = otsu(image)
else:
threshold = entropy(image)
else:
if use_weighted_variance:
t1, t2 = otsu3(image)
else:
t1,t2 = entropy3(image)
threshold = t1 if assign_middle_to_foreground else t2
threshold = inverse_log_transform(threshold, d)
return threshold
def run(self, workspace):
image = workspace.image_set.get_image(self.image_name.value,
must_be_grayscale = True)
orig_pixels = image.pixel_data
if image.has_mask:
mask = image.mask
else:
mask = np.ones(orig_pixels.shape,bool)
if self.method == M_SOBEL:
if self.direction == E_ALL:
output_pixels = sobel(orig_pixels, mask)
elif self.direction == E_HORIZONTAL:
output_pixels = hsobel(orig_pixels, mask)
elif self.direction == E_VERTICAL:
output_pixels = vsobel(orig_pixels, mask)
else:
raise NotImplementedError("Unimplemented direction for Sobel: %s",self.direction.value)
elif self.method == M_LOG:
sigma = self.get_sigma()
size = int(sigma * 4)+1
output_pixels = laplacian_of_gaussian(orig_pixels, mask, size, sigma)
elif self.method == M_VARIANCE:
sigma = self.get_sigma()
size = int(sigma)+1
output_pixels = variance_transform(orig_pixels, size, mask)
elif self.method == M_PREWITT:
if self.direction == E_ALL:
output_pixels = prewitt(orig_pixels)
elif self.direction == E_HORIZONTAL:
output_pixels = hprewitt(orig_pixels, mask)
elif self.direction == E_VERTICAL:
output_pixels = vprewitt(orig_pixels, mask)
else:
raise NotImplementedError("Unimplemented direction for Prewitt: %s",self.direction.value)
elif self.method == M_CANNY:
high_threshold = self.manual_threshold.value
low_threshold = self.low_threshold.value
if (self.wants_automatic_low_threshold.value or
self.wants_automatic_threshold.value):
sobel_image = sobel(orig_pixels, mask)
low, high = otsu3(sobel_image[mask])
if self.wants_automatic_low_threshold.value:
low_threshold = low * self.threshold_adjustment_factor.value
if self.wants_automatic_threshold.value:
high_threshold = high * self.threshold_adjustment_factor.value
output_pixels = canny(orig_pixels,mask, self.get_sigma(),
low_threshold,
high_threshold)
elif self.method == M_ROBERTS:
output_pixels = roberts(orig_pixels, mask)
else:
raise NotImplementedError("Unimplemented edge detection method: %s"%
self.method.value)
output_image = cpi.Image(output_pixels, parent_image = image)
workspace.image_set.add(self.output_image_name.value, output_image)
if self.show_window:
workspace.display_data.orig_pixels = orig_pixels
workspace.display_data.output_pixels = output_pixels
def run(self, workspace):
image = workspace.image_set.get_image(self.image_name.value,
must_be_grayscale=True)
orig_pixels = image.pixel_data
if image.has_mask:
mask = image.mask
else:
mask = np.ones(orig_pixels.shape, bool)
if self.method == M_SOBEL:
if self.direction == E_ALL:
output_pixels = sobel(orig_pixels, mask)
elif self.direction == E_HORIZONTAL:
output_pixels = hsobel(orig_pixels, mask)
elif self.direction == E_VERTICAL:
output_pixels = vsobel(orig_pixels, mask)
else:
raise NotImplementedError(
"Unimplemented direction for Sobel: %s",
self.direction.value)
elif self.method == M_LOG:
sigma = self.get_sigma()
size = int(sigma * 4) + 1
output_pixels = laplacian_of_gaussian(orig_pixels, mask, size,
sigma)
elif self.method == M_PREWITT:
if self.direction == E_ALL:
output_pixels = prewitt(orig_pixels)
elif self.direction == E_HORIZONTAL:
output_pixels = hprewitt(orig_pixels, mask)
elif self.direction == E_VERTICAL:
output_pixels = vprewitt(orig_pixels, mask)
else:
raise NotImplementedError(
"Unimplemented direction for Prewitt: %s",
self.direction.value)
elif self.method == M_CANNY:
high_threshold = self.manual_threshold.value
low_threshold = self.low_threshold.value
if (self.wants_automatic_low_threshold.value
or self.wants_automatic_threshold.value):
sobel_image = sobel(orig_pixels, mask)
low, high = otsu3(sobel_image[mask])
if self.wants_automatic_low_threshold.value:
low_threshold = low * self.threshold_adjustment_factor.value
if self.wants_automatic_threshold.value:
high_threshold = high * self.threshold_adjustment_factor.value
output_pixels = canny(orig_pixels, mask, self.get_sigma(),
low_threshold, high_threshold)
elif self.method == M_ROBERTS:
output_pixels = roberts(orig_pixels, mask)
else:
raise NotImplementedError(
"Unimplemented edge detection method: %s" % self.method.value)
output_image = cpi.Image(output_pixels, parent_image=image)
workspace.image_set.add(self.output_image_name.value, output_image)
if self.show_window:
workspace.display_data.orig_pixels = orig_pixels
workspace.display_data.output_pixels = output_pixels
def test_08_otsu3(self):
"""Test 3-class Otsu with three normal distributions"""
r = np.random.RandomState()
r.seed(8)
x1 = r.normal(0.2, 0.1, 10000)
x2 = r.normal(0.5, 0.25, 5000)
x3 = r.normal(0.8, 0.1, 5000)
data = np.hstack((x1, x2, x3))
data = data[(data > 0) & (data < 1)]
threshold1, threshold2 = otsu3(data)
self.assertTrue(threshold1 > 0.2)
self.assertTrue(threshold1 < 0.5)
self.assertTrue(threshold2 > 0.5)
self.assertTrue(threshold2 < 0.8)
def test_08_otsu3(self):
'''Test 3-class Otsu with three normal distributions'''
r = np.random.RandomState()
r.seed(8)
x1 = r.normal(.2, .1, 10000)
x2 = r.normal(.5, .25, 5000)
x3 = r.normal(.8, .1, 5000)
data = np.hstack((x1, x2, x3))
data = data[(data > 0) & (data < 1)]
threshold1, threshold2 = otsu3(data)
self.assertTrue(threshold1 > .2)
self.assertTrue(threshold1 < .5)
self.assertTrue(threshold2 > .5)
self.assertTrue(threshold2 < .8)
def test_08_otsu3(self):
'''Test 3-class Otsu with three normal distributions'''
r = np.random.RandomState()
r.seed(8)
x1 = r.normal(.2, .1, 10000)
x2 = r.normal(.5, .25, 5000)
x3 = r.normal(.8, .1, 5000)
data = np.hstack((x1, x2, x3))
data = data[(data > 0) & (data < 1)]
threshold1, threshold2 = otsu3(data)
self.assertTrue(threshold1 > .2)
self.assertTrue(threshold1 < .5)
self.assertTrue(threshold2 > .5)
self.assertTrue(threshold2 < .8)
def test_06_01_canny(self):
'''Test the canny method'''
i,j = np.mgrid[-20:20,-20:20]
image = np.logical_and(i > j, i**2+j**2 < 300).astype(np.float32)
np.random.seed(0)
image = image *.5 + np.random.uniform(size=image.shape)*.3
image = np.ascontiguousarray(image, np.float32)
workspace, module = self.make_workspace(image)
module.method.value = F.M_CANNY
module.wants_automatic_threshold.value = True
module.wants_automatic_low_threshold.value = True
module.wants_automatic_sigma.value = True
module.run(workspace)
output = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
t1,t2 = otsu3(FIL.sobel(image))
result = FIL.canny(image, np.ones(image.shape,bool), 1.0, t1, t2)
self.assertTrue(np.all(output.pixel_data == result))
def test_06_01_canny(self):
'''Test the canny method'''
i,j = np.mgrid[-20:20,-20:20]
image = np.logical_and(i > j, i**2+j**2 < 300).astype(np.float32)
np.random.seed(0)
image = image *.5 + np.random.uniform(size=image.shape)*.3
image = np.ascontiguousarray(image, np.float32)
workspace, module = self.make_workspace(image)
module.method.value = F.M_CANNY
module.wants_automatic_threshold.value = True
module.wants_automatic_low_threshold.value = True
module.wants_automatic_sigma.value = True
module.run(workspace)
output = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
t1,t2 = otsu3(FIL.sobel(image))
result = FIL.canny(image, np.ones(image.shape,bool), 1.0, t1, t2)
self.assertTrue(np.all(output.pixel_data == result))
def test_05_03_otsu3_wv_low(self):
'''Test the three-class otsu, weighted variance middle = background'''
np.random.seed(0)
image = np.hstack((np.random.exponential(1.5,size=300),
np.random.poisson(15,size=300),
np.random.poisson(30,size=300))).astype(np.float32)
image.shape=(30,30)
image = stretch(image)
limage, d = T.log_transform(image)
t1,t2 = otsu3(limage)
threshold = T.inverse_log_transform(t2, d)
expected = image > threshold
workspace, module = self.make_workspace(image)
module.binary.value = A.BINARY
module.threshold_method.value = T.TM_OTSU_GLOBAL
module.use_weighted_variance.value = I.O_WEIGHTED_VARIANCE
module.two_class_otsu.value = I.O_THREE_CLASS
module.assign_middle_to_foreground.value = I.O_BACKGROUND
module.run(workspace)
output = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
self.assertTrue(np.all(output.pixel_data == expected))
def test_05_03_otsu3_wv_low(self):
'''Test the three-class otsu, weighted variance middle = background'''
np.random.seed(0)
image = np.hstack((np.random.exponential(1.5,size=300),
np.random.poisson(15,size=300),
np.random.poisson(30,size=300))).astype(np.float32)
image.shape=(30,30)
image = stretch(image)
limage, d = T.log_transform(image)
t1,t2 = otsu3(limage)
threshold = T.inverse_log_transform(t2, d)
expected = image > threshold
workspace, module = self.make_workspace(image)
module.binary.value = A.BINARY
module.threshold_method.value = T.TM_OTSU_GLOBAL
module.use_weighted_variance.value = I.O_WEIGHTED_VARIANCE
module.two_class_otsu.value = I.O_THREE_CLASS
module.assign_middle_to_foreground.value = I.O_BACKGROUND
module.run(workspace)
output = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
self.assertTrue(np.all(output.pixel_data == expected))
def test_05_04_otsu3_wv_high(self):
'''Test the three-class otsu, weighted variance middle = foreground'''
np.random.seed(0)
image = np.hstack((np.random.exponential(1.5,size=300),
np.random.poisson(15,size=300),
np.random.poisson(30,size=300)))
image.shape=(30,30)
image = stretch(image)
limage, d = T.log_transform(image)
t1,t2 = otsu3(limage)
threshold = T.inverse_log_transform(t1, d)
workspace, module = self.make_workspace(image)
module.binary.value = A.BINARY
module.threshold_scope.value = I.TS_GLOBAL
module.threshold_method.value = T.TM_OTSU
module.use_weighted_variance.value = I.O_WEIGHTED_VARIANCE
module.two_class_otsu.value = I.O_THREE_CLASS
module.assign_middle_to_foreground.value = I.O_FOREGROUND
module.run(workspace)
m = workspace.measurements
m_threshold = m[cpmeas.IMAGE, I.FF_ORIG_THRESHOLD % module.get_measurement_objects_name()]
self.assertAlmostEqual(m_threshold, threshold)
def run(self, workspace):
image = workspace.image_set.get_image(self.image_name.value,
must_be_grayscale = True)
orig_pixels = image.pixel_data
if image.has_mask:
mask = image.mask
else:
mask = np.ones(orig_pixels.shape,bool)
if self.method == M_SOBEL:
if self.direction == E_ALL:
output_pixels = sobel(orig_pixels, mask)
elif self.direction == E_HORIZONTAL:
output_pixels = hsobel(orig_pixels, mask)
elif self.direction == E_VERTICAL:
output_pixels = vsobel(orig_pixels, mask)
else:
raise NotImplementedError("Unimplemented direction for Sobel: %s",self.direction.value)
elif self.method == M_LOG:
sigma = self.get_sigma()
size = int(sigma * 4)+1
output_pixels = laplacian_of_gaussian(orig_pixels, mask, size, sigma)
elif self.method == M_PREWITT:
if self.direction == E_ALL:
output_pixels = prewitt(orig_pixels)
elif self.direction == E_HORIZONTAL:
output_pixels = hprewitt(orig_pixels, mask)
elif self.direction == E_VERTICAL:
output_pixels = vprewitt(orig_pixels, mask)
else:
raise NotImplementedError("Unimplemented direction for Prewitt: %s",self.direction.value)
elif self.method == M_CANNY:
high_threshold = self.manual_threshold.value
low_threshold = self.low_threshold.value
if (self.wants_automatic_low_threshold.value or
self.wants_automatic_threshold.value):
sobel_image = sobel(orig_pixels, mask)
low, high = otsu3(sobel_image[mask])
if self.wants_automatic_low_threshold.value:
low_threshold = low * self.threshold_adjustment_factor.value
if self.wants_automatic_threshold.value:
high_threshold = high * self.threshold_adjustment_factor.value
output_pixels = canny(orig_pixels,mask, self.get_sigma(),
low_threshold,
high_threshold)
elif self.method == M_ROBERTS:
output_pixels = roberts(orig_pixels, mask)
else:
raise NotImplementedError("Unimplemented edge detection method: %s"%
self.method.value)
if not workspace.frame is None:
figure = workspace.create_or_find_figure(title="EnhanceEdges, image cycle #%d"%(
workspace.measurements.image_set_number),subplots=(2,2))
figure.subplot_imshow_grayscale(0,0, orig_pixels,
"Original: %s"%
self.image_name.value)
if self.method == M_CANNY:
# Canny is binary
figure.subplot_imshow_bw(0,1, output_pixels,
self.output_image_name.value,
sharex = figure.subplot(0,0),
sharey = figure.subplot(0,0))
else:
figure.subplot_imshow_grayscale(0,1,output_pixels,
self.output_image_name.value,
sharex = figure.subplot(0,0),
sharey = figure.subplot(0,0))
color_image = np.zeros((output_pixels.shape[0],
output_pixels.shape[1],3))
color_image[:,:,0] = stretch(orig_pixels)
color_image[:,:,1] = stretch(output_pixels)
figure.subplot_imshow(1,0, color_image,"Composite image",
sharex = figure.subplot(0,0),
sharey = figure.subplot(0,0))
output_image = cpi.Image(output_pixels, parent_image = image)
workspace.image_set.add(self.output_image_name.value, output_image)
def run(self, workspace):
image = workspace.image_set.get_image(self.image_name.value,
must_be_grayscale=True)
orig_pixels = image.pixel_data
if image.has_mask:
mask = image.mask
else:
mask = np.ones(orig_pixels.shape, bool)
if self.method == M_SOBEL:
if self.direction == E_ALL:
output_pixels = sobel(orig_pixels, mask)
elif self.direction == E_HORIZONTAL:
output_pixels = hsobel(orig_pixels, mask)
elif self.direction == E_VERTICAL:
output_pixels = vsobel(orig_pixels, mask)
else:
raise NotImplementedError(
"Unimplemented direction for Sobel: %s",
self.direction.value)
elif self.method == M_LOG:
sigma = self.get_sigma()
size = int(sigma * 4) + 1
output_pixels = laplacian_of_gaussian(orig_pixels, mask, size,
sigma)
elif self.method == M_PREWITT:
if self.direction == E_ALL:
output_pixels = prewitt(orig_pixels)
elif self.direction == E_HORIZONTAL:
output_pixels = hprewitt(orig_pixels, mask)
elif self.direction == E_VERTICAL:
output_pixels = vprewitt(orig_pixels, mask)
else:
raise NotImplementedError(
"Unimplemented direction for Prewitt: %s",
self.direction.value)
elif self.method == M_CANNY:
high_threshold = self.manual_threshold.value
low_threshold = self.low_threshold.value
if (self.wants_automatic_low_threshold.value
or self.wants_automatic_threshold.value):
sobel_image = sobel(orig_pixels, mask)
low, high = otsu3(sobel_image[mask])
if self.wants_automatic_low_threshold.value:
low_threshold = low * self.threshold_adjustment_factor.value
if self.wants_automatic_threshold.value:
high_threshold = high * self.threshold_adjustment_factor.value
output_pixels = canny(orig_pixels, mask, self.get_sigma(),
low_threshold, high_threshold)
elif self.method == M_ROBERTS:
output_pixels = roberts(orig_pixels, mask)
else:
raise NotImplementedError(
"Unimplemented edge detection method: %s" % self.method.value)
if not workspace.frame is None:
figure = workspace.create_or_find_figure(
title="EnhanceEdges, image cycle #%d" %
(workspace.measurements.image_set_number),
subplots=(2, 2))
figure.subplot_imshow_grayscale(
0, 0, orig_pixels, "Original: %s" % self.image_name.value)
if self.method == M_CANNY:
# Canny is binary
figure.subplot_imshow_bw(0,
1,
output_pixels,
self.output_image_name.value,
sharex=figure.subplot(0, 0),
sharey=figure.subplot(0, 0))
else:
figure.subplot_imshow_grayscale(0,
1,
output_pixels,
self.output_image_name.value,
sharex=figure.subplot(0, 0),
sharey=figure.subplot(0, 0))
color_image = np.zeros(
(output_pixels.shape[0], output_pixels.shape[1], 3))
color_image[:, :, 0] = stretch(orig_pixels)
color_image[:, :, 1] = stretch(output_pixels)
figure.subplot_imshow(1,
0,
color_image,
"Composite image",
sharex=figure.subplot(0, 0),
sharey=figure.subplot(0, 0))
output_image = cpi.Image(output_pixels, parent_image=image)
workspace.image_set.add(self.output_image_name.value, output_image)