Macenko pca out of bounds fix (#1007)

* Fix out-of-bounds bug in argpercentile * Include argpercentile tests * Update tests/test_color_deconvolution.py --------- Co-authored-by: gum31714 <[email protected]>
DigitalSlideArchive · Jul 12, 2023 · a076c44 · a076c44
1 parent 15262df
commit a076c44
Show file tree

Hide file tree

Showing 2 changed files with 26 additions and 1 deletion.
diff --git a/histomicstk/preprocessing/color_deconvolution/separate_stains_macenko_pca.py b/histomicstk/preprocessing/color_deconvolution/separate_stains_macenko_pca.py
@@ -121,5 +121,5 @@ def _get_angles(m):
 def argpercentile(arr, p):
     """Calculate index in arr of element nearest the pth percentile."""
     # Index corresponding to percentile
-    i = int(p * arr.size + 0.5)
+    i = min(int(p * arr.size + 0.5), arr.size - 1)
     return numpy.argpartition(arr, i)[i]
diff --git a/tests/test_color_deconvolution.py b/tests/test_color_deconvolution.py
@@ -2,6 +2,8 @@
 import skimage.io
 
 from histomicstk.preprocessing import color_deconvolution as htk_dcv
+from histomicstk.preprocessing.color_deconvolution.separate_stains_macenko_pca import \
+    argpercentile as htk_ap
 
 from .datastore import datastore
 
@@ -20,6 +22,29 @@ def test_macenko(self):
 
         np.testing.assert_allclose(w, w_expected, atol=1e-6)
 
+    def test_argpercentile(self):
+        arr = np.array([])
+        with np.testing.assert_raises(IndexError):
+            htk_ap(arr, 0.5)
+
+        arr = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
+
+        w = htk_ap(arr, 0.5)
+        w_expected = 5
+        np.testing.assert_equal(w, w_expected)
+
+        w = htk_ap(arr, 0.1)
+        w_expected = 1
+        np.testing.assert_equal(w, w_expected)
+
+        w = htk_ap(arr, 0.0)
+        w_expected = 0
+        np.testing.assert_equal(w, w_expected)
+
+        w = htk_ap(arr, 0.99)
+        w_expected = 9
+        np.testing.assert_equal(w, w_expected)
+
 
 class TestColorDeconvolution: