Update GeodesicSegmentation CLI #1496
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sarthakpati
suggested changes
May 28, 2022
| thresholder->SetInput(geosOutput); | ||
| thresholder->SetOutsideValue(0); | ||
| thresholder->SetInsideValue(1); | ||
| thresholder->SetLowerThreshold(threshold); | ||
| thresholder->SetUpperThreshold(maxVal); | ||
| thresholder->SetLowerThreshold(0); |
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Suggested change
| thresholder->SetLowerThreshold(0); | |
| thresholder->SetLowerThreshold(threshold); |
This should use threshold instead of a hard-coded 0.
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Your suggestion is what it was before. The geodesic distance map that is created before the thresholding step is represented as increasing values away from the original segmentation/seeds. So setting it as you suggest will yield a 1 label in everything outside the predicted region of interest.
I tested this and compared to the GUI version with my changes, and this makes them consistent.
| thresholder->SetLowerThreshold(threshold); | ||
| thresholder->SetUpperThreshold(maxVal); | ||
| thresholder->SetLowerThreshold(0); | ||
| thresholder->SetUpperThreshold(threshold); |
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Suggested change
| thresholder->SetUpperThreshold(threshold); | |
| thresholder->SetUpperThreshold(maxVal); |
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Fixes an issue where GeodesicSegmentation's CLI was broken -- threshold values could never be read, the generated masks/distance maps were not being written for any voxels other than what was already labelled, and the threshold filter was wrongly inverted.