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Add click for image_uncertainty_per_region #94

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

Add click for image_uncertainty_per_region #94

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11 changes: 10 additions & 1 deletion gatetools/bin/gt_image_uncertainty.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,10 @@

@click.option('--sigma', default=False, is_flag=True, help='By default, uncertainty is normalized, unc = sigma/x. By using this option, the output is *not* normalized, sigma=sqrt(var) is computed.')

@click.option('--label','-l', help='label map filename to compute uncertainty by region')

@gt.add_options(gt.common_options)
def gt_image_uncertainty(filenames, nevents, output, counts, by_slice, threshold, efficiency, sigma, verbose, **kwargs):
def gt_image_uncertainty(filenames, nevents, output, counts, by_slice, threshold, efficiency, sigma, label, verbose, **kwargs):
'''
Compute relative statistical uncertainty image for a list of
images. Images are summed before computing the the uncertainty.
Expand All @@ -56,6 +58,10 @@ def gt_image_uncertainty(filenames, nevents, output, counts, by_slice, threshold
uncertainty. Only consider pixel values greater than threshold %
of the max value in the image.

Option '-l' with the path to a label map will compute the
uncertainty by region. Each region is represented by one label
in the label map.

Example1:
gt_image_uncertainty run.XYZ/output_*/dose-Edep.mhd -o u.mhd -N 100000000

Expand Down Expand Up @@ -113,6 +119,9 @@ def gt_image_uncertainty(filenames, nevents, output, counts, by_slice, threshold
# compute uncertainty history by hitory
if by_slice:
uncertainty, m, nb = gt.image_uncertainty_by_slice(filenames, sfilenames, nevents, sigma_flag, threshold)
elif label is not None:
label_image = itk.imread(label)
uncertainty = gt.image_uncertainty_per_region(filenames, sfilenames, label_image, nevents, sigma_flag, threshold)
else:
uncertainty = gt.image_uncertainty(filenames, sfilenames, nevents, sigma_flag, threshold)
else:
Expand Down