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test(morphology): vet DIAMETER_EQUAL_PERIMETER + ORIENTATION + EROSIONS_2_VANISH -> 80/113 #391

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test(morphology): vet DIAMETER_EQUAL_PERIMETER + ORIENTATION + EROSIONS_2_VANISH -> 80/113 #391

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8 changes: 4 additions & 4 deletions tests/test_all.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -1012,14 +1012,14 @@ TEST(TEST_NYXUS, TEST_SHAPE2D_CONTOUR_FEATURES)
ASSERT_NO_THROW(test_shape2d_contour_features());
}

TEST(TEST_NYXUS, TEST_SHAPE2D_VERIFIABLE_WITH_3P_BUILTIN_ORACLE_CONTOUR_DIAMETER_EQUAL_PERIMETER)
TEST(TEST_NYXUS, TEST_SHAPE2D_CONVEX_HULL_FEATURES)
{
ASSERT_NO_THROW(test_shape2d_verifiable_with_3p_builtin_oracle_contour_diameter_equal_perimeter());
ASSERT_NO_THROW(test_shape2d_convex_hull_features());
}

TEST(TEST_NYXUS, TEST_SHAPE2D_CONVEX_HULL_FEATURES)
TEST(TEST_NYXUS, TEST_SHAPE2D_SKIMAGE_ORIENTATION_AND_EROSIONS)
{
ASSERT_NO_THROW(test_shape2d_convex_hull_features());
ASSERT_NO_THROW(test_shape2d_skimage_orientation_and_erosions());
}

TEST(TEST_NYXUS, TEST_SHAPE2D_VERIFIABLE_WITH_3P_BUILTIN_ORACLE_EXTREMA_FEATURES)
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23 changes: 14 additions & 9 deletions tests/test_morphology_regression.h
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Expand Up @@ -34,7 +34,8 @@ void test_shape2d_ellipse_features()
assert_unvetted_no_direct_oracle_shape2d_feature(fvals, Nyxus::Feature2D::MINOR_AXIS_LENGTH, "MINOR_AXIS_LENGTH");
assert_unvetted_no_direct_oracle_shape2d_feature(fvals, Nyxus::Feature2D::ELONGATION, "ELONGATION");
assert_unvetted_no_direct_oracle_shape2d_feature(fvals, Nyxus::Feature2D::ECCENTRICITY, "ECCENTRICITY");
assert_unvetted_no_direct_oracle_shape2d_feature(fvals, Nyxus::Feature2D::ORIENTATION, "ORIENTATION");
// ORIENTATION is vetted vs scikit-image in test_morphology_skimage.h; ROUNDNESS is vetted by
// documented-formula conformance in test_shape2d_documented_formula_conformance_no_external_oracle.
assert_unvetted_no_direct_oracle_shape2d_feature(fvals, Nyxus::Feature2D::ROUNDNESS, "ROUNDNESS");
}

Expand Down Expand Up @@ -85,6 +86,12 @@ void test_shape2d_documented_formula_conformance_no_external_oracle()
const double round_formula = 4.0 * A / (PI * major * major);
ASSERT_NEAR(fvals[static_cast<int>(Nyxus::Feature2D::ROUNDNESS)][0], round_formula, 1e-9)
<< "ROUNDNESS does not match 4A/(pi*major^2)";

// DIAMETER_EQUAL_PERIMETER = P / pi (contour.cpp) -- diameter of the circle with the same
// perimeter. Pure double arithmetic on the vetted PERIMETER, so it conforms exactly.
const double dep_formula = P / PI;
ASSERT_NEAR(fvals[static_cast<int>(Nyxus::Feature2D::DIAMETER_EQUAL_PERIMETER)][0], dep_formula, 1e-9)
<< "DIAMETER_EQUAL_PERIMETER does not match PERIMETER/pi";
}

void test_shape2d_unvetted_no_direct_oracle_radius_features()
Expand All @@ -97,13 +104,8 @@ void test_shape2d_unvetted_no_direct_oracle_radius_features()
assert_unvetted_no_direct_oracle_shape2d_feature(fvals, Nyxus::Feature2D::ROI_RADIUS_MEDIAN, "ROI_RADIUS_MEDIAN");
}

void test_shape2d_verifiable_with_3p_builtin_oracle_contour_diameter_equal_perimeter()
{
std::vector<std::vector<double>> fvals;
calculate_shape2d_feature_values(fvals);

assert_verifiable_with_3p_builtin_oracle_shape2d_feature(fvals, Nyxus::Feature2D::DIAMETER_EQUAL_PERIMETER, "DIAMETER_EQUAL_PERIMETER");
}
// DIAMETER_EQUAL_PERIMETER is now vetted by documented-formula conformance (P/pi) in
// test_shape2d_documented_formula_conformance_no_external_oracle.

void test_shape2d_verifiable_with_3p_builtin_oracle_fractal_circle_features()
{
Expand All @@ -120,9 +122,12 @@ void test_shape2d_verifiable_with_3p_builtin_oracle_geodetic_thickness_erosion_f
{
std::vector<std::vector<double>> fvals;
calculate_shape2d_feature_values(fvals);
// GEODETIC_LENGTH stays regression: geo_len_thickness.cpp truncates PERIMETER to size_t and uses
// integer division, so its value (10.0) deviates ~11% from the real-valued rectangle formula
// (~11.13); vetting it analytically would bake in the truncation. THICKNESS is vetted vs imea.
assert_verifiable_with_3p_builtin_oracle_shape2d_feature(fvals, Nyxus::Feature2D::GEODETIC_LENGTH, "GEODETIC_LENGTH");
assert_verifiable_with_3p_builtin_oracle_shape2d_feature(fvals, Nyxus::Feature2D::THICKNESS, "THICKNESS");
assert_verifiable_with_3p_builtin_oracle_shape2d_feature(fvals, Nyxus::Feature2D::EROSIONS_2_VANISH, "EROSIONS_2_VANISH");
// EROSIONS_2_VANISH is now vetted vs scikit-image (square(3)) in test_morphology_skimage.h.
}

// ---------------------------------------------------------------------------------------------------
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19 changes: 19 additions & 0 deletions tests/test_morphology_skimage.h
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Expand Up @@ -13,3 +13,22 @@ void test_shape2d_convex_hull_features()
assert_verifiable_with_3p_builtin_oracle_shape2d_feature(fvals, Nyxus::Feature2D::CONVEX_HULL_AREA, "CONVEX_HULL_AREA", 100.0);
assert_verifiable_with_3p_builtin_oracle_shape2d_feature(fvals, Nyxus::Feature2D::SOLIDITY, "SOLIDITY", 100.0);
}

// ORIENTATION and EROSIONS_2_VANISH vetted vs scikit-image (tests/vetting/oracles/gen_morphology_skimage.py).
// ORIENTATION: skimage regionprops orientation is measured from the row axis; Nyxus measures the same
// ellipse's major axis from the x axis, so NYXUS == 90 - degrees(skimage.orientation) = 70.4173944984
// (matches to 10 decimals -- the angle is invariant to the pixel-size second-moment correction that makes
// the AXIS LENGTHS differ ~1.4%, which is why MAJOR/MINOR/ECCENTRICITY stay regression).
// EROSIONS_2_VANISH: Nyxus' 3x3 (8-connected) structuring element == skimage square(3); the count (1)
// matches, and disk(1)/4-connected gives 2, so the test also pins the connectivity convention.
void test_shape2d_skimage_orientation_and_erosions()
{
std::vector<std::vector<double>> fvals;
calculate_shape2d_feature_values(fvals);

// skimage-derived goldens (90 - degrees(regionprops.orientation); square(3) erosion count)
ASSERT_NEAR(fvals[static_cast<int>(Nyxus::Feature2D::ORIENTATION)][0], 70.4173944984207, 1e-3)
<< "ORIENTATION does not match 90 - skimage.orientation(deg)";
ASSERT_NEAR(fvals[static_cast<int>(Nyxus::Feature2D::EROSIONS_2_VANISH)][0], 1.0, 1e-9)
<< "EROSIONS_2_VANISH does not match skimage square(3) erosion count";
}
6 changes: 3 additions & 3 deletions tests/vetting/coverage_report.md
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Expand Up @@ -2,8 +2,8 @@

_Generated by check_coverage.py from oracle_coverage.csv. Do not edit by hand._

Features vetted by >=1 oracle: 604/758 (80%)
regression: 154 untested: 0
Features vetted by >=1 oracle: 607/758 (80%)
regression: 151 untested: 0

| family | total | vetted | regression | untested |
|---|---|---|---|---|
Expand All @@ -17,7 +17,7 @@ regression: 154 untested: 0
| imq | 6 | 0 | 6 | 0 |
| intensity_histogram | 47 | 47 | 0 | 0 |
| moments | 180 | 118 | 62 | 0 |
| morphology | 113 | 77 | 36 | 0 |
| morphology | 113 | 80 | 33 | 0 |
| neighbor | 9 | 2 | 7 | 0 |
| ngldm | 38 | 20 | 18 | 0 |
| ngtdm | 10 | 10 | 0 | 0 |
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