fix(morphology): geodetic length/thickness from real perimeter (was size_t-truncated) - #392
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fix(morphology): geodetic length/thickness from real perimeter (was size_t-truncated)#392darkclad wants to merge 2 commits into
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July 23, 2026 12:59
…NS_2_VANISH -> 80/113
Vet three more 2D morphology features against analytic / scikit-image oracles
(morphology 77 -> 80), and document why four others in the "future-vettable" list
are not cleanly promotable.
Promoted:
- DIAMETER_EQUAL_PERIMETER -> analytic. == PERIMETER/pi (contour.cpp), pure double
arithmetic on the vetted PERIMETER; recomputed at 1e-9 in the existing
documented-formula-conformance test (same treatment as CIRCULARITY/ROUNDNESS).
- ORIENTATION -> skimage. skimage regionprops measures the major-axis angle from the
row axis; Nyxus measures the same ellipse from the x axis, so NYXUS ==
90 - degrees(skimage.orientation) = 70.4174. Matches to 10 decimals because the
ellipse angle is invariant to the pixel-size second-moment correction (it shifts
mu20 and mu02 equally). New gtest test_shape2d_skimage_orientation_and_erosions +
tests/vetting/oracles/gen_morphology_skimage.py.
- EROSIONS_2_VANISH -> skimage. Nyxus' 3x3 (8-connected) erosion count ==
skimage binary_erosion(square(3)) = 1; disk(1)/4-connected gives 2, so the test
also pins the connectivity convention.
Documented (stay regression, with reasons in the registry notes):
- GEODETIC_LENGTH: 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 -- a latent
precision issue to fix first.
- ROI_RADIUS_MEAN/MAX: mean/max per-pixel min SQUARED distance to the ROI's own
contour pixels (roi_radius.cpp); scipy distance_transform_edt uses a different
reference (distance to background, not squared), so no standard tool reproduces it.
- EROSIONS_2_VANISH_COMPLEMENT: degenerate 0 on this fixture; needs a holed fixture.
- MAJOR/MINOR_AXIS_LENGTH, ECCENTRICITY: ~1.4% moment-normalization gap vs skimage,
left regression.
gtest 717/717; pytest 72 passed (7 arrow fails are the tiff-only local build, not
regressions). Coverage regenerated (604 -> 607 / 758).
…ize_t-truncated) geo_len_thickness.cpp assigned PERIMETER (a double) into a size_t and then used integer division, truncating the perimeter to its floor and rounding every intermediate term. On the 8x8 shape2d fixture this made GEODETIC_LENGTH 10.0 and THICKNESS 3.0 -- ~11% off the rectangle-model formula (geodetic ~11.13, thickness ~2.34). Keep perimeter and area as double and use floating-point division, so both features equal the documented side lengths of the rectangle with the same area and perimeter (the roots of x^2 - (P/2)x + A = 0). Vet both by documented-formula conformance (like CIRCULARITY / DIAMETER_EQUAL_PERIMETER): GEODETIC_LENGTH == P/4 + sqrt(P^2/16 - A), THICKNESS == P/2 - GEODETIC_LENGTH, recomputed at 1e-9 from the vetted AREA + PERIMETER in test_shape2d_documented_formula_conformance_no_external_oracle. GEODETIC_LENGTH regression -> vetted (analytic); THICKNESS imea -> analytic (its prior imea row was tracker-only -- test_morphology_imea.h never existed -- and the loose 1000x snapshot had pinned the truncated 3.0). Goldens updated; the redundant loose geodetic gtest removed. morphology 80 -> 81. gtest 716/716; pytest 72 passed (7 arrow fails are the tiff-only local build; no Python test covers these features). Coverage 607 -> 608 / 758.
vjaganat90
approved these changes
Jul 29, 2026
| {"GEODETIC_LENGTH", 10.0}, | ||
| {"THICKNESS", 3.0}, | ||
| // Real-valued rectangle-model roots after the geo_len_thickness.cpp perimeter-truncation fix | ||
| // (were the integer-truncated 10.0 / 3.0). Now vetted by analytic conformance in |
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GREAT! I have always suspected these
| } | ||
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| TEST(TEST_NYXUS, TEST_SHAPE2D_VERIFIABLE_WITH_3P_BUILTIN_ORACLE_CONTOUR_DIAMETER_EQUAL_PERIMETER) | ||
| TEST(TEST_NYXUS, TEST_SHAPE2D_CONVEX_HULL_FEATURES) |
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Not a blocker. If all the oracle supported tests are in tests/vetting then we should releax the naming of test groups and fixtures to original names, We should discuss this offline.
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geo_len_thickness.cpp assigned PERIMETER (a double) into a size_t and then used integer
division, truncating the perimeter to its floor and rounding every intermediate term. On
the 8x8 shape2d fixture this made GEODETIC_LENGTH 10.0 and THICKNESS 3.0 -- ~11% off the
rectangle-model formula (geodetic ~11.13, thickness ~2.34). Keep perimeter and area as
double and use floating-point division, so both features equal the documented side lengths
of the rectangle with the same area and perimeter (the roots of x^2 - (P/2)x + A = 0).
Vet both by documented-formula conformance (like CIRCULARITY / DIAMETER_EQUAL_PERIMETER):
GEODETIC_LENGTH == P/4 + sqrt(P^2/16 - A), THICKNESS == P/2 - GEODETIC_LENGTH, recomputed
at 1e-9 from the vetted AREA + PERIMETER in
test_shape2d_documented_formula_conformance_no_external_oracle. GEODETIC_LENGTH
regression -> vetted (analytic); THICKNESS imea -> analytic (its prior imea row was
tracker-only -- test_morphology_imea.h never existed -- and the loose 1000x snapshot had
pinned the truncated 3.0). Goldens updated; the redundant loose geodetic gtest removed.
morphology 80 -> 81.
gtest 716/716; pytest 72 passed (7 arrow fails are the tiff-only local build; no Python
test covers these features). Coverage 607 -> 608 / 758.