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feat: merge rate metric (#138)
Co-authored-by: anna-grim <[email protected]>
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‎demo/results-overview.txt‎

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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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% Split: 1.1996
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% Omit: 4.5086
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% Merged: 0.0000
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Edge Accuracy: 95.4914
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ERL: 180.8849
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Normalized ERL: 0.3949
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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% Split: 1.1996
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% Omit: 4.5086
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% Merged: 0.0000
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Edge Accuracy: 95.4914
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ERL: 180.8849
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Normalized ERL: 0.3949
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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% Split: 1.1996
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% Omit: 4.5086
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% Merged: 0.0000
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Edge Accuracy: 95.4914
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ERL: 180.8849
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Normalized ERL: 0.3949
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: 0.0000
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 95.4914
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ERL: 180.8849
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Normalized ERL: 0.3949
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 0.0000
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# Merges: 0.0000
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Split Rate: 0.0000
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Merge Rate: 0.0000
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% Split Edges: 0.9218
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% Omit Edges: 0.9218
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% Merged Edges: 9.0909
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Edge Accuracy: 89.9873
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ERL: 0.0000
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Normalized ERL: 0.0000
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Total Results...
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# Splits: 0
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# Merges: 0
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Average Results...
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# Splits: 0.0000
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# Merges: 0.0000
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Split Rate: 0.0000
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Merge Rate: 0.0000
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% Split Edges: 0.9218
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% Omit Edges: 0.9218
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% Merged Edges: 0.0000
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Edge Accuracy: 99.0782
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ERL: 331.6691
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Normalized ERL: 1.0000
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Total Results...
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# Splits: 0
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# Merges: 0
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Average Results...
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# Splits: 0.0000
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# Merges: 0.0000
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Split Rate: 0.0000
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Merge Rate: 0.0000
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% Split Edges: 0.9218
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% Omit Edges: 3.6209
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 130.9891
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Normalized ERL: 0.6413
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% Merged e: 0.0000
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Total Results...
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# Splits: 0
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: 0.0000
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 180.8849
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Normalized ERL: 0.3949
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% Merged e: 0.0000
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: 0.0000
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 180.8849
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Normalized ERL: 0.3949
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% Merged e: 0.0000
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 0.0000
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# Merges: 0.0000
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Split Rate: 0.0000
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 1.1996
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 842.7172
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Normalized ERL: 1.0000
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% Merged e: 0.0000
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Total Results...
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# Splits: 0
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: inf
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 180.8849
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Normalized ERL: 0.3949
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% Merged e: 0.0000
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: inf
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 180.8849
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Normalized ERL: 0.3949
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% Merged e: 0.0000
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: inf
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 180.8849
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Normalized ERL: 0.3949
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% Merged e: 0.0000
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: inf
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 180.8849
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Normalized ERL: 0.3949
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% Merged e: 0.0000
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: 100.5656
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 180.8849
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Normalized ERL: 0.3949
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% Merged e: 0.0000
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: 114.6940
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 180.8849
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Normalized ERL: 0.3949
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% Merged e: 0.0000
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: 114.6940
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 180.8849
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Normalized ERL: 0.3949
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% Merged e: 0.0000
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000
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Split Rate: 114.6940
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Merge Rate: 0.0000
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% Split Edges: 1.1996
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% Omit Edges: 4.5086
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% Merged Edges: 0.0000
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Edge Accuracy: 0.0000
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ERL: 180.8849
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Normalized ERL: 0.3949
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% Merged e: 0.0000
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Total Results...
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# Splits: 31
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# Merges: 0
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Average Results...
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# Splits: 7.9680
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# Merges: 0.0000

‎demo/results.csv‎

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,# Splits,# Merges,Split Rate,Merge Rate,% Split Edges,% Omit Edges,% Merged Edges,Edge Accuracy,ERL,Normalized ERL,GT Run Length
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SNT_Data-002,0,,84.08376161857129,,0.0,0.0,0.0,100.0,84.08,1.0,84.08
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SNT_Data-035,0,,163.37074041968344,,0.0,0.0,0.0,100.0,163.37,1.0,163.37
2+
SNT_Data-002,0,,84.0837616185713,,0.0,0.0,0.0,100.0,84.08,1.0,84.08
3+
SNT_Data-035,0,,163.37074041968347,,0.0,0.0,0.0,100.0,163.37,1.0,163.37
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SNT_Data-037,1,,211.98055903143307,,0.98,1.96,0.0,98.04,184.57,0.8585,214.98
5-
SNT_Data-038,1,,251.78664303157592,,0.83,1.65,0.0,98.35,144.38,0.5667,254.79
6-
SNT_Data-041,4,,55.46881994891758,,2.83,7.55,0.0,92.45,52.62,0.2286,230.17
5+
SNT_Data-038,1,,251.78664303157586,,0.83,1.65,0.0,98.35,144.38,0.5667,254.79
6+
SNT_Data-041,4,,55.46881994891756,,2.83,7.55,0.0,92.45,52.62,0.2286,230.17
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SNT_Data-043,2,,46.354813254114404,,1.92,9.62,0.0,90.38,35.32,0.3334,105.96
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SNT_Data-051,0,,106.56843799568803,,0.0,0.0,0.0,100.0,106.57,1.0,106.57
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SNT_Data-052,6,,99.17738848187405,,1.37,6.48,0.0,93.52,265.1,0.4184,633.57
9+
SNT_Data-052,6,,99.17738848187408,,1.37,6.48,0.0,93.52,265.1,0.4184,633.57
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SNT_Data-053,15,,98.71530688808681,,1.31,4.46,0.0,95.54,207.79,0.1343,1547.45
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SNT_Data-062,2,,105.18979564964228,,0.9,8.11,0.0,91.89,116.9,0.5144,227.24
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SNT_Data-074,0,,80.17991450259146,,0.0,0.0,0.0,100.0,80.18,1.0,80.18
12+
SNT_Data-074,0,,80.17991450259144,,0.0,0.0,0.0,100.0,80.18,1.0,80.18

‎src/segmentation_skeleton_metrics/skeleton_graph.py‎

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class SkeletonGraph(nx.Graph):
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"""
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A subclass of the NetworkX.Graph designed for graphs built from SWC files.
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This class extends the functionality of the standard Graph by adding
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This class extends the functionality of the standard Graph class by adding
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support for handling node labels and voxel coordinates. In this subclass,
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node IDs serve as direct indices for accessing the labels and voxels
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attributes.
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anisotropy : numpy.ndarray
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Image to physical coordinates scaling factors to account for the
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anisotropy of the microscope.
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run_length : float
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Physical path length of the graph.
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filename : str
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Filename of SWC file that graph is built from.
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is_groundtruth : bool
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Indication of whether this graph corresponds to a ground truth
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tracing.
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labels : numpy.ndarray
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A 1D array that contains a label value associated with each node.
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run_length : float
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Physical path length of the graph.
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voxels : numpy.ndarray
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A 3D array that contains a voxel coordinate for each node.
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"""
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is_groundtruth : bool, optional
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Indication of whether this graph corresponds to a ground truth
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tracing. Default is False.
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None
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"""
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# Call parent class
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super(SkeletonGraph, self).__init__()
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Returns
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-------
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numpy.ndarray
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A 1D array of node IDs that have the specified label.
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Node IDs that have the specified label.
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"""
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return np.where(self.labels == label)[0]
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