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test(neighbor): oracle-vet 6 features (analytic + CellProfiler) -> neighbor 8/9 #390

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test(neighbor): oracle-vet 6 features (analytic + CellProfiler) -> neighbor 8/9 #390

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10 changes: 6 additions & 4 deletions tests/test_all.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,8 @@
#include "test_remaining2d_common.h"
#include "test_zernike_regression.h"
#include "test_neighbor_regression.h"
#include "test_neighbor_cellprofiler.h"
#include "test_neighbor_analytic.h"
#include "test_initialization_mechanics.h"
#include "test_glcm_ibsi.h"
#include "test_gldm_ibsi.h"
Expand Down Expand Up @@ -1147,14 +1149,14 @@ TEST(TEST_NYXUS, TEST_NEIGHBORHOOD2D_CLOSEST_NEIGHBORS)
ASSERT_NO_THROW(test_neighborhood2d_closest_neighbors());
}

TEST(TEST_NYXUS, TEST_NEIGHBORHOOD2D_UNVETTED_NO_DIRECT_ORACLE_CLOSEST_NEIGHBOR_ANGLES)
TEST(TEST_NYXUS, TEST_NEIGHBORHOOD2D_CELLPROFILER_COUNTS_FIRST_DISTANCE)
{
ASSERT_NO_THROW(test_neighborhood2d_unvetted_no_direct_oracle_closest_neighbor_angles());
ASSERT_NO_THROW(test_neighborhood2d_cellprofiler_counts_and_first_distance());
}

TEST(TEST_NYXUS, TEST_NEIGHBORHOOD2D_UNVETTED_NO_DIRECT_ORACLE_ANGLE_STATS)
TEST(TEST_NYXUS, TEST_NEIGHBORHOOD2D_ANALYTIC_SECOND_DISTANCE_AND_ANGLES)
{
ASSERT_NO_THROW(test_neighborhood2d_unvetted_no_direct_oracle_neighbor_angle_stats());
ASSERT_NO_THROW(test_neighborhood2d_analytic_second_distance_and_angles());
}


Expand Down
89 changes: 89 additions & 0 deletions tests/test_neighbor_analytic.h
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@@ -0,0 +1,89 @@
#pragma once

// ANALYTIC oracle for the 2D neighbor second-distance + angle features.
// Given the neighbor graph (which CellProfiler vets, see test_neighbor_cellprofiler.h),
// these six features are deterministic closed forms of the ROI centroids, so an
// independent numpy recomputation of Nyxus' documented formulas IS the oracle
// (same analytic-conformance basis as CIRCULARITY / intensity_histogram). Goldens
// and the formula derivation are in tests/vetting/oracles/gen_neighbor_analytic.py,
// which validates them to double precision against these values; asserted at 1e-4.
//
// Why not CellProfiler for these: CP's AngleBetweenNeighbors is the angle SUBTENDED
// at an object by its two neighbors, not Nyxus' absolute atan2 direction angle; and
// CP's SecondClosestDistance is the 2nd-closest of ANY object, whereas Nyxus reports
// the 2nd-closest neighbor WITHIN the search radius (0 when <2 in-radius neighbors).

#include <gtest/gtest.h>

#include "test_neighbor_regression.h" // shared fixture builder calculate_neighborhood2d_feature_values

static std::unordered_map<int, std::unordered_map<std::string, double>> neighbor2d_analytic_golden_by_label{
{1, {
{"CLOSEST_NEIGHBOR2_DIST", 2.54950975679639},
{"CLOSEST_NEIGHBOR1_ANG", 0.0},
{"CLOSEST_NEIGHBOR2_ANG", 191.30993247402},
{"ANG_BW_NEIGHBORS_MEAN", 132.172516881495},
{"ANG_BW_NEIGHBORS_STDDEV", 115.230018010206},
{"ANG_BW_NEIGHBORS_MODE", 0.0},
}},
{2, {
{"CLOSEST_NEIGHBOR2_DIST", 0.0},
{"CLOSEST_NEIGHBOR1_ANG", 11.3099324740202},
{"CLOSEST_NEIGHBOR2_ANG", 0.0},
{"ANG_BW_NEIGHBORS_MEAN", 11.3099324740202},
{"ANG_BW_NEIGHBORS_STDDEV", 0.0},
{"ANG_BW_NEIGHBORS_MODE", 11.0},
}},
{3, {
{"CLOSEST_NEIGHBOR2_DIST", 0.0},
{"CLOSEST_NEIGHBOR1_ANG", 78.6900675259798},
{"CLOSEST_NEIGHBOR2_ANG", 0.0},
{"ANG_BW_NEIGHBORS_MEAN", 78.6900675259798},
{"ANG_BW_NEIGHBORS_STDDEV", 0.0},
{"ANG_BW_NEIGHBORS_MODE", 79.0},
}},
{4, {
{"CLOSEST_NEIGHBOR2_DIST", 0.0},
{"CLOSEST_NEIGHBOR1_ANG", 180.0},
{"CLOSEST_NEIGHBOR2_ANG", 0.0},
{"ANG_BW_NEIGHBORS_MEAN", 180.0},
{"ANG_BW_NEIGHBORS_STDDEV", 0.0},
{"ANG_BW_NEIGHBORS_MODE", 180.0},
}},
{5, {
{"CLOSEST_NEIGHBOR2_DIST", 0.0},
{"CLOSEST_NEIGHBOR1_ANG", 258.69006752598},
{"CLOSEST_NEIGHBOR2_ANG", 0.0},
{"ANG_BW_NEIGHBORS_MEAN", 258.69006752598},
{"ANG_BW_NEIGHBORS_STDDEV", 0.0},
{"ANG_BW_NEIGHBORS_MODE", 259.0},
}}
};

static void assert_neighbor2d_analytic(
const std::unordered_map<int, LR>& roiData,
int label,
Nyxus::Feature2D feature,
const std::string& feature_name)
{
SCOPED_TRACE(std::string("ANALYTIC__") + feature_name + "__L" + std::to_string(label));
ASSERT_TRUE(neighbor2d_analytic_golden_by_label[label].count(feature_name) > 0);
ASSERT_NEAR(roiData.at(label).fvals[static_cast<int>(feature)][0],
neighbor2d_analytic_golden_by_label[label][feature_name], 1e-4);
}

void test_neighborhood2d_analytic_second_distance_and_angles()
{
std::unordered_map<int, LR> roiData;
calculate_neighborhood2d_feature_values(roiData);

for (int label : {1, 2, 3, 4, 5})
{
assert_neighbor2d_analytic(roiData, label, Nyxus::Feature2D::CLOSEST_NEIGHBOR2_DIST, "CLOSEST_NEIGHBOR2_DIST");
assert_neighbor2d_analytic(roiData, label, Nyxus::Feature2D::CLOSEST_NEIGHBOR1_ANG, "CLOSEST_NEIGHBOR1_ANG");
assert_neighbor2d_analytic(roiData, label, Nyxus::Feature2D::CLOSEST_NEIGHBOR2_ANG, "CLOSEST_NEIGHBOR2_ANG");
assert_neighbor2d_analytic(roiData, label, Nyxus::Feature2D::ANG_BW_NEIGHBORS_MEAN, "ANG_BW_NEIGHBORS_MEAN");
assert_neighbor2d_analytic(roiData, label, Nyxus::Feature2D::ANG_BW_NEIGHBORS_STDDEV, "ANG_BW_NEIGHBORS_STDDEV");
assert_neighbor2d_analytic(roiData, label, Nyxus::Feature2D::ANG_BW_NEIGHBORS_MODE, "ANG_BW_NEIGHBORS_MODE");
}
}
49 changes: 49 additions & 0 deletions tests/test_neighbor_cellprofiler.h
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@@ -0,0 +1,49 @@
#pragma once

// CellProfiler oracle for the 2D neighbor-graph features NUM_NEIGHBORS and
// CLOSEST_NEIGHBOR1_DIST. The real cellprofiler.modules.MeasureObjectNeighbors
// module (Adjacent method) was run on this fixture; CP reproduces Nyxus exactly for
// both features. Goldens + the offline CP run are in
// tests/vetting/oracles/gen_neighbor_cellprofiler.py; asserted at 1e-4.
//
// PERCENT_TOUCHING is NOT vetted here: CP and Nyxus use different definitions
// (Nyxus = contour pixels 8-adjacent to a neighbor / contour length; CP = object
// outline pixels overlapping a disk(distance+0.5)-dilated neighbor / perimeter), and
// no CP distance method reproduces Nyxus (diverges on 3/5 ROIs). It stays a
// regression snapshot in test_neighbor_regression.h.

#include <gtest/gtest.h>

#include "test_neighbor_regression.h" // shared fixture builder calculate_neighborhood2d_feature_values

static std::unordered_map<int, std::unordered_map<std::string, double>> neighbor2d_cellprofiler_golden_by_label{
{1, {{"NUM_NEIGHBORS", 4.0}, {"CLOSEST_NEIGHBOR1_DIST", 2.5}}},
{2, {{"NUM_NEIGHBORS", 1.0}, {"CLOSEST_NEIGHBOR1_DIST", 2.54950975679639}}},
{3, {{"NUM_NEIGHBORS", 1.0}, {"CLOSEST_NEIGHBOR1_DIST", 2.54950975679639}}},
{4, {{"NUM_NEIGHBORS", 1.0}, {"CLOSEST_NEIGHBOR1_DIST", 2.5}}},
{5, {{"NUM_NEIGHBORS", 1.0}, {"CLOSEST_NEIGHBOR1_DIST", 2.54950975679639}}}
};

static void assert_neighbor2d_cellprofiler(
const std::unordered_map<int, LR>& roiData,
int label,
Nyxus::Feature2D feature,
const std::string& feature_name)
{
SCOPED_TRACE(std::string("CELLPROFILER__") + feature_name + "__L" + std::to_string(label));
ASSERT_TRUE(neighbor2d_cellprofiler_golden_by_label[label].count(feature_name) > 0);
ASSERT_NEAR(roiData.at(label).fvals[static_cast<int>(feature)][0],
neighbor2d_cellprofiler_golden_by_label[label][feature_name], 1e-4);
}

void test_neighborhood2d_cellprofiler_counts_and_first_distance()
{
std::unordered_map<int, LR> roiData;
calculate_neighborhood2d_feature_values(roiData);

for (int label : {1, 2, 3, 4, 5})
{
assert_neighbor2d_cellprofiler(roiData, label, Nyxus::Feature2D::NUM_NEIGHBORS, "NUM_NEIGHBORS");
assert_neighbor2d_cellprofiler(roiData, label, Nyxus::Feature2D::CLOSEST_NEIGHBOR1_DIST, "CLOSEST_NEIGHBOR1_DIST");
}
}
79 changes: 5 additions & 74 deletions tests/test_neighbor_regression.h
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Expand Up @@ -47,43 +47,11 @@ static std::unordered_map<int, std::unordered_map<std::string, double>> unvetted
}}
};

static std::unordered_map<int, std::unordered_map<std::string, double>> unvetted_nyxus_regression_neighbor2d_angle_feature_golden_values_by_label{
{1, {
{"CLOSEST_NEIGHBOR1_ANG", 0.0},
{"CLOSEST_NEIGHBOR2_ANG", 191.30993247402},
{"ANG_BW_NEIGHBORS_MEAN", 132.172516881495},
{"ANG_BW_NEIGHBORS_STDDEV", 115.230018010206},
{"ANG_BW_NEIGHBORS_MODE", 0.0},
}},
{2, {
{"CLOSEST_NEIGHBOR1_ANG", 11.3099324740202},
{"CLOSEST_NEIGHBOR2_ANG", 0.0},
{"ANG_BW_NEIGHBORS_MEAN", 11.3099324740202},
{"ANG_BW_NEIGHBORS_STDDEV", 0.0},
{"ANG_BW_NEIGHBORS_MODE", 11.0},
}},
{3, {
{"CLOSEST_NEIGHBOR1_ANG", 78.6900675259798},
{"CLOSEST_NEIGHBOR2_ANG", 0.0},
{"ANG_BW_NEIGHBORS_MEAN", 78.6900675259798},
{"ANG_BW_NEIGHBORS_STDDEV", 0.0},
{"ANG_BW_NEIGHBORS_MODE", 79.0},
}},
{4, {
{"CLOSEST_NEIGHBOR1_ANG", 180.0},
{"CLOSEST_NEIGHBOR2_ANG", 0.0},
{"ANG_BW_NEIGHBORS_MEAN", 180.0},
{"ANG_BW_NEIGHBORS_STDDEV", 0.0},
{"ANG_BW_NEIGHBORS_MODE", 180.0},
}},
{5, {
{"CLOSEST_NEIGHBOR1_ANG", 258.69006752598},
{"CLOSEST_NEIGHBOR2_ANG", 0.0},
{"ANG_BW_NEIGHBORS_MEAN", 258.69006752598},
{"ANG_BW_NEIGHBORS_STDDEV", 0.0},
{"ANG_BW_NEIGHBORS_MODE", 259.0},
}}
};
// NOTE: the closest-neighbor angles and the angle-between-neighbors stats are now
// vetted at tight tolerance by the ANALYTIC oracle in test_neighbor_analytic.h
// (independent numpy recomputation of Nyxus' atan2 direction-angle formulas); the
// second-closest distance likewise. This regression file keeps only the fixture
// builder + the PERCENT_TOUCHING snapshot (the one feature with no promotable oracle).

static Fsettings make_neighbors2d_settings()
{
Expand Down Expand Up @@ -154,19 +122,6 @@ static void assert_neighbor2d_feature(
ASSERT_TRUE(agrees_gt(roiData.at(label).fvals[static_cast<int>(feature)][0], unvetted_nyxus_regression_neighbor2d_distance_feature_golden_values_by_label[label][feature_name], frac_tolerance));
}

static void assert_unvetted_no_direct_oracle_neighbor2d_feature(
const std::unordered_map<int, LR>& roiData,
int label,
Nyxus::Feature2D feature,
const std::string& feature_name,
double frac_tolerance = 1000.0)
{
SCOPED_TRACE(std::string("UNVETTED_NO_DIRECT_ORACLE__") + feature_name);
ASSERT_TRUE(unvetted_nyxus_regression_neighbor2d_angle_feature_golden_values_by_label.count(label) > 0);
ASSERT_TRUE(unvetted_nyxus_regression_neighbor2d_angle_feature_golden_values_by_label[label].count(feature_name) > 0);
ASSERT_TRUE(agrees_gt(roiData.at(label).fvals[static_cast<int>(feature)][0], unvetted_nyxus_regression_neighbor2d_angle_feature_golden_values_by_label[label][feature_name], frac_tolerance));
}

void test_neighborhood2d_counts_and_touching()
{
std::unordered_map<int, LR> roiData;
Expand Down Expand Up @@ -211,27 +166,3 @@ void test_neighborhood2d_closest_neighbors()
}
}

void test_neighborhood2d_unvetted_no_direct_oracle_closest_neighbor_angles()
{
std::unordered_map<int, LR> roiData;
calculate_neighborhood2d_feature_values(roiData);

for (int label : {1, 2, 3, 4, 5})
{
assert_unvetted_no_direct_oracle_neighbor2d_feature(roiData, label, Nyxus::Feature2D::CLOSEST_NEIGHBOR1_ANG, "CLOSEST_NEIGHBOR1_ANG");
assert_unvetted_no_direct_oracle_neighbor2d_feature(roiData, label, Nyxus::Feature2D::CLOSEST_NEIGHBOR2_ANG, "CLOSEST_NEIGHBOR2_ANG");
}
}

void test_neighborhood2d_unvetted_no_direct_oracle_neighbor_angle_stats()
{
std::unordered_map<int, LR> roiData;
calculate_neighborhood2d_feature_values(roiData);

for (int label : {1, 2, 3, 4, 5})
{
assert_unvetted_no_direct_oracle_neighbor2d_feature(roiData, label, Nyxus::Feature2D::ANG_BW_NEIGHBORS_MEAN, "ANG_BW_NEIGHBORS_MEAN");
assert_unvetted_no_direct_oracle_neighbor2d_feature(roiData, label, Nyxus::Feature2D::ANG_BW_NEIGHBORS_STDDEV, "ANG_BW_NEIGHBORS_STDDEV");
assert_unvetted_no_direct_oracle_neighbor2d_feature(roiData, label, Nyxus::Feature2D::ANG_BW_NEIGHBORS_MODE, "ANG_BW_NEIGHBORS_MODE");
}
}
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: 610/758 (80%)
regression: 148 untested: 0

| family | total | vetted | regression | untested |
|---|---|---|---|---|
Expand All @@ -18,7 +18,7 @@ regression: 154 untested: 0
| intensity_histogram | 47 | 47 | 0 | 0 |
| moments | 180 | 118 | 62 | 0 |
| morphology | 113 | 77 | 36 | 0 |
| neighbor | 9 | 2 | 7 | 0 |
| neighbor | 9 | 8 | 1 | 0 |
| ngldm | 38 | 20 | 18 | 0 |
| ngtdm | 10 | 10 | 0 | 0 |
| radial | 3 | 0 | 3 | 0 |
Expand Down
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