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Add lesion-wise metrics #50

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Add lesion-wise metrics #50

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083054b
Add the lesion-wise metrics proposed in https://github.com/ivadomed/M…
valosekj May 31, 2024
ad23622
Change lesion PPV to 0.0 in case of non-empty reference and empty pre…
valosekj Jun 4, 2024
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3 changes: 3 additions & 0 deletions compute_metrics/compute_metrics_reloaded.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,9 @@
'nsd': 'Normalized surface distance (NSD)',
'vol_diff': 'Volume difference',
'rel_vol_error': 'Relative volume error (RVE)',
'lesion_ppv': 'Lesion wise positive predictive value (PPV)',
'lesion_sensitivity': 'Lesion wise sensitivity',
'lesion_f1_score': 'Lesion wise F1 score',
}


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37 changes: 29 additions & 8 deletions tests/test_compute_metrics_reloaded.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
from compute_metrics.compute_metrics_reloaded import compute_metrics_single_subject
import tempfile

METRICS = ['dsc', 'fbeta', 'nsd', 'vol_diff', 'rel_vol_error']
METRICS = ['dsc', 'fbeta', 'nsd', 'vol_diff', 'rel_vol_error', 'lesion_ppv', 'lesion_sensitivity', 'lesion_f1_score']


class TestComputeMetricsReloaded(unittest.TestCase):
Expand Down Expand Up @@ -59,7 +59,10 @@ def test_empty_ref_and_pred(self):
'fbeta': 1,
'nsd': np.nan,
'rel_vol_error': 0,
'vol_diff': np.nan}}
'vol_diff': np.nan,
'lesion_ppv': 1.0,
'lesion_sensitivity': 1.0,
'lesion_f1_score': 1.0}}

# Create empty reference
self.create_dummy_nii(self.ref_file, np.zeros((10, 10, 10)))
Expand All @@ -81,7 +84,10 @@ def test_empty_ref(self):
'fbeta': 0,
'nsd': 0.0,
'rel_vol_error': 100,
'vol_diff': np.inf}}
'vol_diff': np.inf,
'lesion_ppv': 0.0,
'lesion_sensitivity': 1.0,
'lesion_f1_score': 0.0}}

# Create empty reference
self.create_dummy_nii(self.ref_file, np.zeros((10, 10, 10)))
Expand All @@ -105,7 +111,10 @@ def test_empty_pred(self):
'fbeta': 0,
'nsd': 0.0,
'rel_vol_error': -100.0,
'vol_diff': 1.0}}
'vol_diff': 1.0,
'lesion_ppv': 0.0,
'lesion_sensitivity': 0.0,
'lesion_f1_score': 0.0}}

# Create non-empty reference
ref = np.zeros((10, 10, 10))
Expand All @@ -129,7 +138,10 @@ def test_non_empty_ref_and_pred(self):
'fbeta': 0.26666667461395266,
'nsd': 0.5373134328358209,
'rel_vol_error': 300.0,
'vol_diff': 3.0}}
'vol_diff': 3.0,
'lesion_ppv': 1.0,
'lesion_sensitivity': 1.0,
'lesion_f1_score': 1.0}}

# Create non-empty reference
ref = np.zeros((10, 10, 10))
Expand All @@ -156,14 +168,20 @@ def test_non_empty_ref_and_pred_multi_class(self):
'vol_diff': 2.0,
'rel_vol_error': 200.0,
'EmptyRef': False,
'EmptyPred': False},
'EmptyPred': False,
'lesion_ppv': 1.0,
'lesion_sensitivity': 1.0,
'lesion_f1_score': 1.0},
2.0: {'dsc': 0.26666666666666666,
'fbeta': 0.26666667461395266,
'nsd': 0.5373134328358209,
'vol_diff': 3.0,
'rel_vol_error': 300.0,
'EmptyRef': False,
'EmptyPred': False}}
'EmptyPred': False,
'lesion_ppv': 1.0,
'lesion_sensitivity': 1.0,
'lesion_f1_score': 1.0}}

# Create non-empty reference
ref = np.zeros((10, 10, 10))
Expand Down Expand Up @@ -191,7 +209,10 @@ def test_non_empty_ref_and_pred_with_full_overlap(self):
'fbeta': 1.0,
'nsd': 1.0,
'rel_vol_error': 0.0,
'vol_diff': 0.0}}
'vol_diff': 0.0,
'lesion_ppv': 1.0,
'lesion_sensitivity': 1.0,
'lesion_f1_score': 1.0}}

# Create non-empty reference
ref = np.zeros((10, 10, 10))
Expand Down
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