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Compute uncertainty by regions #93

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Merged
tbaudier merged 1 commit into from
Mar 21, 2025
Merged

Compute uncertainty by regions #93

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50 changes: 49 additions & 1 deletion gatetools/image_uncertainty.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,37 @@ def image_uncertainty(img_list=[], img_squared_list=[], N=0, sigma_flag=False, t
img_uncertainty.CopyInformation(img_sum)
return img_uncertainty

def image_uncertainty_per_region(img_list=[], img_squared_list=[], img_label=None, N=0, sigma_flag=False, threshold=0):
check_N(N)

# Check label image
if img_label is None:
image_uncertainty(img_list, img_squared_list, N, sigma_flag, threshold)
return

# Get the sums
img_sum = gt.image_sum(img_list)
img_sq_sum = gt.image_sum(img_squared_list)

# View as np
np_sum = itk.array_view_from_image(img_sum)
np_sq_sum = itk.array_view_from_image(img_sq_sum)
np_label = itk.array_from_image(img_label).astype(int)

# Group values by label
max_label = np.max(np_label)
np_sum_by_label = np.bincount(np_label.ravel(), weights=np_sum.ravel(), minlength=max_label + 1)
np_sq_sum_by_label = np.bincount(np_label.ravel(), weights=np_sq_sum.ravel(), minlength=max_label + 1)

# Compute relative uncertainty [Chetty 2006]
t = np.max(np_sum_by_label)*threshold
uncertainty = relative_uncertainty(np_sum_by_label, np_sq_sum_by_label, N, t)

# create a text file to save uncertainty by region
with open('uncertainty_by_region.txt', 'w') as f:
for i, value in enumerate(uncertainty):
f.write(f"{i}\t{value}\n")
return uncertainty

def image_uncertainty_by_slice(img_list=[], img_squared_list=[], N=0, sigma_flag=False, threshold=0):
check_N(N)
Expand Down Expand Up @@ -213,7 +244,7 @@ def test_image_uncertainty(self):
bytesNew = fnew.read()
new_hash = hashlib.sha256(bytesNew).hexdigest()
self.assertTrue("0e1f8e0f0d7d7d3921c726dc33409345e6d9b8bfcc53b797d67f8b48997fa1a5" == new_hash)
print(tmpdirpath)
shutil.rmtree(tmpdirpath)
def test_image_uncertainty_by_slice(self):
x = np.arange(0, 1, 0.01)
y = np.arange(0, 1, 0.01)
Expand Down Expand Up @@ -270,3 +301,20 @@ def test_image_uncertainty_Poisson_by_slice(self):
new_hash = hashlib.sha256(bytesNew).hexdigest()
self.assertTrue("cb58fb2f5490546bb83b9e0e51ce1d87b13eab2f0f4ebddc4e9c767c8b98e57b" == new_hash)
shutil.rmtree(tmpdirpath)
def test_image_uncertainty_per_region(self):
x = np.arange(0, 1, 0.01)
y = np.arange(0, 1, 0.01)
z = np.arange(0, 1, 0.01)
xx, yy, zz = np.meshgrid(x, y, z)
npImage = 10*xx+4.5
npsImage = 10*xx**2+9*xx+2.85
pattern = np.arange(9)
pattern_array = np.tile(pattern, npImage.size // pattern.size + 1)[:npImage.size]
pattern_array = pattern_array.reshape(npImage.shape)
image = itk.image_from_array(np.float64(npImage))
images = [image]
simage = itk.image_from_array(np.float64(npsImage))
simages = [simage]
limage = itk.image_from_array(np.float64(pattern_array))
uncertainty = image_uncertainty_per_region(images, simages, limage, N=1000000000000)
self.assertTrue(np.allclose(uncertainty, np.array([0.00103301, 0.00103302, 0.00103302, 0.00103302, 0.00103302, 0.00103301, 0.00103301, 0.00103301, 0.00103301])))