fix(chords): correct max-chord angle index and all-chords histogram s…

src/nyx/features/chords.cpp

@@ -78,7 +78,9 @@ void ChordsFeature::calculate (LR & r, const Fsettings& s)
 	maxchords_min_angle = MCang[idxmin];
 
 	auto iteMax = std::max_element(MC.begin(), MC.end());
-	auto idxmax = std::distance(MC.begin(), iteMin);
+	// FIX: index the LONGEST max-chord (iteMax). Previously used iteMin, so
+	// maxchords_max_angle always equalled maxchords_min_angle.
+	auto idxmax = std::distance(MC.begin(), iteMax);
 	maxchords_max_angle = MCang[idxmax];
 
 	// Analyze all chords
@@ -91,16 +93,20 @@ void ChordsFeature::calculate (LR & r, const Fsettings& s)
 	allchords_mean = mom2.mean();
 	allchords_stddev = mom2.std();
 
-	histo.initialize_uniques(MC); 
-	allchords_mode = histo.get_mode(); 
-	allchords_median = histo.get_median(); 
+	// FIX: build the all-chords histogram from AC (all chords). Previously it
+	// reused MC (max-chords), so all-chords mode/median were the max-chords ones.
+	histo.initialize_uniques(AC);
+	allchords_mode = histo.get_mode();
+	allchords_median = histo.get_median();
 
 	iteMin = std::min_element(AC.begin(), AC.end());
 	idxmin = std::distance(AC.begin(), iteMin);
 	allchords_min_angle = ACang[idxmin];
 
 	iteMax = std::max_element(AC.begin(), AC.end());
-	idxmax = std::distance(AC.begin(), iteMin);
+	// FIX: index the LONGEST all-chord (iteMax). Previously used iteMin, so
+	// allchords_max_angle always equalled allchords_min_angle.
+	idxmax = std::distance(AC.begin(), iteMax);
 	allchords_max_angle = ACang[idxmax];
 }
 

tests/python/test_feature_oracle.py

@@ -0,0 +1,68 @@
+"""Regression / bug-exposure tests for 2D feature defects found during oracle validation
+(2026-06). These exercise the PRODUCTION featurize() path on ROIs *with background* and at
+the DEFAULT settings - the conditions the C++ unit tests miss.
+
+This module covers the chords max-angle / AC-vs-MC defect (bug #16).
+"""
+import re
+from pathlib import Path
+import numpy as np
+import pytest
+import nyxus
+
+
+# ----------------------------- helpers --------------------------------------
+def _canonical_roi():
+    """The pixelIntensityFeaturesTestData ROI from tests/test_data.h - the same irregular
+    154-px region the C++ tests use, which reproduces the shape/moment defects. Falls back to
+    an L-shape if the header can't be read."""
+    hdr = Path(__file__).resolve().parent.parent / "test_data.h"
+    try:
+        txt = hdr.read_text(encoding="utf-8", errors="replace")
+        body = re.search(r"pixelIntensityFeaturesTestData\[\]\s*=\s*\{(.*?)\};", txt, re.S).group(1)
+        pts = [(int(x), int(y), int(v)) for x, y, v in
+               re.findall(r"\{\s*(\d+)\s*,\s*(\d+)\s*,\s*(\d+)\s*\}", body)]
+        W = max(p[0] for p in pts) + 2
+        H = max(p[1] for p in pts) + 2
+        inten = np.zeros((H, W), np.uint32)
+        label = np.zeros((H, W), np.uint32)
+        for x, y, v in pts:
+            inten[y, x] = v
+            label[y, x] = 1
+        return inten, label
+    except Exception:
+        return None
+
+
+def _run(features, inten, label, **kw):
+    nyx = nyxus.Nyxus(features=features, n_feature_calc_threads=1, **kw)
+    df = nyx.featurize(inten.astype(np.float64), label.astype(np.uint32),
+                       intensity_names=["i"], label_names=["l"])
+    return df  # one row per label
+
+
+def _one(features, inten, label, **kw):
+    return _run(features, inten, label, **kw).iloc[0]
+
+
+# ============================ CHORDS ========================================
+def test_chord_max_angle_distinct_from_min():
+    """Bug #16 (FIXED): chords.cpp computed the max-chord angle index from iteMin
+    (`idxmax = distance(begin, iteMin)`), so MAXCHORDS_MAX_ANG was ALWAYS equal to
+    MAXCHORDS_MIN_ANG (same copy-paste error for ALLCHORDS). When the longest and shortest
+    chords have different lengths they occur at different orientations, so the max- and
+    min-angle must differ. Also exercised: ALLCHORDS mode/median were built from the
+    max-chords histogram (MC) instead of all chords (AC)."""
+    c = _canonical_roi()
+    if c is None:
+        pytest.skip("canonical ROI (tests/test_data.h) not available")
+    inten, label = c
+    row = _one(["MAXCHORDS_MAX", "MAXCHORDS_MIN", "MAXCHORDS_MAX_ANG", "MAXCHORDS_MIN_ANG",
+                "ALLCHORDS_MAX", "ALLCHORDS_MIN", "ALLCHORDS_MAX_ANG", "ALLCHORDS_MIN_ANG"],
+               inten, label)
+    if row["MAXCHORDS_MAX"] != row["MAXCHORDS_MIN"]:
+        assert row["MAXCHORDS_MAX_ANG"] != row["MAXCHORDS_MIN_ANG"], \
+            "MAXCHORDS max-angle == min-angle (idxmax=iteMin copy-paste bug regressed)"
+    if row["ALLCHORDS_MAX"] != row["ALLCHORDS_MIN"]:
+        assert row["ALLCHORDS_MAX_ANG"] != row["ALLCHORDS_MIN_ANG"], \
+            "ALLCHORDS max-angle == min-angle (idxmax=iteMin copy-paste bug regressed)"

tests/test_2d_remaining_features.h

@@ -51,19 +51,21 @@ static std::unordered_map<std::string, double> oracle_3p_remaining2d_feature_gol
 	{"MAXCHORDS_STDDEV", 0.94451324138833304},
 	{"ALLCHORDS_MAX", 6.0},
 	{"ALLCHORDS_MIN", 1.0},
-	{"ALLCHORDS_MEDIAN", 4.0},
+	// FIXED (chords.cpp histo built from MC): all-chords median/mode now computed over ALL chords, not max-chords
+	{"ALLCHORDS_MEDIAN", 3.0},
 	{"ALLCHORDS_MEAN", 2.9134615384615379},
-	{"ALLCHORDS_MODE", 4.0},
+	{"ALLCHORDS_MODE", 3.0},
 	{"ALLCHORDS_STDDEV", 1.3446086298393252},
 };
 
 static std::unordered_map<std::string, double> unvetted_nyxus_regression_remaining2d_feature_golden_values{
 	{"POLYGONALITY_AVE", 2.0833333333333357},
 	{"HEXAGONALITY_AVE", 6.4262878058432173},
 	{"HEXAGONALITY_STDDEV", 0.31438281411429858},
-	{"MAXCHORDS_MAX_ANG", 0.94247779607693793},
+	// FIXED (chords.cpp idxmax used iteMin): max-angle now indexes the longest chord (angle 0), not the min
+	{"MAXCHORDS_MAX_ANG", 0.0},
 	{"MAXCHORDS_MIN_ANG", 0.94247779607693793},
-	{"ALLCHORDS_MAX_ANG", 0.15707963267948966},
+	{"ALLCHORDS_MAX_ANG", 0.0},
 	{"ALLCHORDS_MIN_ANG", 0.15707963267948966},
 };