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(1) more features matching Cellprofiler | (2) unnamed feature no. 252 (NGLDM_DCP) fixed #169

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Nov 14, 2023
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(1) more features matching Cellprofiler | (2) unnamed feature no. 252 (NGLDM_DCP) fixed #169

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21 changes: 21 additions & 0 deletions src/nyx/environment.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -589,8 +589,11 @@ void Environment::process_feature_list()
SPAT_MOMENT_10,
SPAT_MOMENT_11,
SPAT_MOMENT_12,
SPAT_MOMENT_13,
SPAT_MOMENT_20,
SPAT_MOMENT_21,
SPAT_MOMENT_22,
SPAT_MOMENT_23,
SPAT_MOMENT_30,

// Weighted spatial moments
Expand All @@ -606,13 +609,22 @@ void Environment::process_feature_list()
WEIGHTED_SPAT_MOMENT_30,

// Central moments
CENTRAL_MOMENT_00,
CENTRAL_MOMENT_01,
CENTRAL_MOMENT_02,
CENTRAL_MOMENT_03,
CENTRAL_MOMENT_10,
CENTRAL_MOMENT_11,
CENTRAL_MOMENT_12,
CENTRAL_MOMENT_13,
CENTRAL_MOMENT_20,
CENTRAL_MOMENT_21,
CENTRAL_MOMENT_22,
CENTRAL_MOMENT_23,
CENTRAL_MOMENT_30,
CENTRAL_MOMENT_31,
CENTRAL_MOMENT_32,
CENTRAL_MOMENT_33,

// Weighted central moments
WEIGHTED_CENTRAL_MOMENT_02,
Expand All @@ -638,8 +650,17 @@ void Environment::process_feature_list()
NORM_SPAT_MOMENT_02,
NORM_SPAT_MOMENT_03,
NORM_SPAT_MOMENT_10,
NORM_SPAT_MOMENT_11,
NORM_SPAT_MOMENT_12,
NORM_SPAT_MOMENT_13,
NORM_SPAT_MOMENT_20,
NORM_SPAT_MOMENT_21,
NORM_SPAT_MOMENT_22,
NORM_SPAT_MOMENT_23,
NORM_SPAT_MOMENT_30,
NORM_SPAT_MOMENT_31,
NORM_SPAT_MOMENT_32,
NORM_SPAT_MOMENT_33,

// Hu's moments 1-7
HU_M1,
Expand Down
21 changes: 21 additions & 0 deletions src/nyx/features/contour.h
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Original file line number Diff line number Diff line change
Expand Up @@ -37,8 +37,11 @@ class ContourFeature: public FeatureMethod
SPAT_MOMENT_10,
SPAT_MOMENT_11,
SPAT_MOMENT_12,
SPAT_MOMENT_13,
SPAT_MOMENT_20,
SPAT_MOMENT_21,
SPAT_MOMENT_22,
SPAT_MOMENT_23,
SPAT_MOMENT_30,
// Weighted spatial moments
WEIGHTED_SPAT_MOMENT_00,
Expand All @@ -52,13 +55,22 @@ class ContourFeature: public FeatureMethod
WEIGHTED_SPAT_MOMENT_21,
WEIGHTED_SPAT_MOMENT_30,
// Central moments
CENTRAL_MOMENT_00,
CENTRAL_MOMENT_01,
CENTRAL_MOMENT_02,
CENTRAL_MOMENT_03,
CENTRAL_MOMENT_10,
CENTRAL_MOMENT_11,
CENTRAL_MOMENT_12,
CENTRAL_MOMENT_13,
CENTRAL_MOMENT_20,
CENTRAL_MOMENT_21,
CENTRAL_MOMENT_22,
CENTRAL_MOMENT_23,
CENTRAL_MOMENT_30,
CENTRAL_MOMENT_31,
CENTRAL_MOMENT_32,
CENTRAL_MOMENT_33,
// Weighted central moments
WEIGHTED_CENTRAL_MOMENT_02,
WEIGHTED_CENTRAL_MOMENT_03,
Expand All @@ -81,8 +93,17 @@ class ContourFeature: public FeatureMethod
NORM_SPAT_MOMENT_02,
NORM_SPAT_MOMENT_03,
NORM_SPAT_MOMENT_10,
NORM_SPAT_MOMENT_11,
NORM_SPAT_MOMENT_12,
NORM_SPAT_MOMENT_13,
NORM_SPAT_MOMENT_20,
NORM_SPAT_MOMENT_21,
NORM_SPAT_MOMENT_22,
NORM_SPAT_MOMENT_23,
NORM_SPAT_MOMENT_30,
NORM_SPAT_MOMENT_31,
NORM_SPAT_MOMENT_32,
NORM_SPAT_MOMENT_33,
// Hu's moments 1-7
HU_M1,
HU_M2,
Expand Down
105 changes: 93 additions & 12 deletions src/nyx/features/image_moments.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -11,23 +11,44 @@ ImageMomentsFeature::ImageMomentsFeature() : FeatureMethod("ImageMomentsFeature"
SPAT_MOMENT_10,
SPAT_MOMENT_11,
SPAT_MOMENT_12,
SPAT_MOMENT_13,
SPAT_MOMENT_20,
SPAT_MOMENT_21,
SPAT_MOMENT_22,
SPAT_MOMENT_23,
SPAT_MOMENT_30,
NORM_SPAT_MOMENT_00,
NORM_SPAT_MOMENT_01,
NORM_SPAT_MOMENT_02,
NORM_SPAT_MOMENT_03,
NORM_SPAT_MOMENT_10,
NORM_SPAT_MOMENT_20,
NORM_SPAT_MOMENT_30,
CENTRAL_MOMENT_00,
CENTRAL_MOMENT_01,
CENTRAL_MOMENT_02,
CENTRAL_MOMENT_03,
CENTRAL_MOMENT_10,
CENTRAL_MOMENT_11,
CENTRAL_MOMENT_12,
CENTRAL_MOMENT_13,
CENTRAL_MOMENT_20,
CENTRAL_MOMENT_21,
CENTRAL_MOMENT_22,
CENTRAL_MOMENT_23,
CENTRAL_MOMENT_30,
CENTRAL_MOMENT_31,
CENTRAL_MOMENT_32,
CENTRAL_MOMENT_33,
NORM_SPAT_MOMENT_00,
NORM_SPAT_MOMENT_01,
NORM_SPAT_MOMENT_02,
NORM_SPAT_MOMENT_03,
NORM_SPAT_MOMENT_10,
NORM_SPAT_MOMENT_11,
NORM_SPAT_MOMENT_12,
NORM_SPAT_MOMENT_13,
NORM_SPAT_MOMENT_20,
NORM_SPAT_MOMENT_21,
NORM_SPAT_MOMENT_22,
NORM_SPAT_MOMENT_23,
NORM_SPAT_MOMENT_30,
NORM_SPAT_MOMENT_31,
NORM_SPAT_MOMENT_32,
NORM_SPAT_MOMENT_33,
NORM_CENTRAL_MOMENT_02,
NORM_CENTRAL_MOMENT_03,
NORM_CENTRAL_MOMENT_11,
Expand Down Expand Up @@ -109,10 +130,10 @@ void ImageMomentsFeature::calculate_via_gpu (LR& r, size_t roi_idx)
std::cerr << "Geometric moments: error sending ROI contour data to GPU-side\n";

ok = ImageMomentsFeature_calculate (
m00, m01, m02, m03, m10, m11, m12, m20, m21, m30, // spatial moments
mu02, mu03, mu11, mu12, mu20, mu21, mu30, // central moments
m00, m01, m02, m03, m10, m11, m12, m13, m20, m21, m22, m23, m30, // spatial moments
mu00, mu01, mu02, mu03, mu10, mu11, mu12, mu13, mu20, mu21, mu22, mu23, mu30, mu31, mu32, mu33, // central moments
nu02, nu03, nu11, nu12, nu20, nu21, nu30, // normalized central moments
w00, w01, w02, w03, w10, w20, w30, // normalized spatial moments
w00, w01, w02, w03, w10, w11, w12, w13, w20, w21, w22, w23, w30, w31, w32, w33, // normalized spatial moments
hm1, hm2, hm3, hm4, hm5, hm6, hm7, // Hu moments
wm00, wm01, wm02, wm03, wm10, wm11, wm12, wm20, wm21, wm30, // weighted spatial moments
wmu02, wmu03, wmu11, wmu12, wmu20, wmu21, wmu30, // weighted central moments
Expand All @@ -137,15 +158,32 @@ void ImageMomentsFeature::osized_add_online_pixel (size_t x, size_t y, uint32_t

void ImageMomentsFeature::save_value(std::vector<std::vector<double>>& fvals)
{
SPAT_MOMENT_00,
SPAT_MOMENT_01,
SPAT_MOMENT_02,
SPAT_MOMENT_03,
SPAT_MOMENT_10,
SPAT_MOMENT_11,
SPAT_MOMENT_12,
SPAT_MOMENT_13,
SPAT_MOMENT_20,
SPAT_MOMENT_21,
SPAT_MOMENT_22,
SPAT_MOMENT_23,
SPAT_MOMENT_30,

fvals[SPAT_MOMENT_00][0] = m00;
fvals[SPAT_MOMENT_01][0] = m01;
fvals[SPAT_MOMENT_02][0] = m02;
fvals[SPAT_MOMENT_03][0] = m03;
fvals[SPAT_MOMENT_10][0] = m10;
fvals[SPAT_MOMENT_11][0] = m11;
fvals[SPAT_MOMENT_12][0] = m12;
fvals[SPAT_MOMENT_13][0] = m13;
fvals[SPAT_MOMENT_20][0] = m20;
fvals[SPAT_MOMENT_21][0] = m21;
fvals[SPAT_MOMENT_22][0] = m22;
fvals[SPAT_MOMENT_23][0] = m23;
fvals[SPAT_MOMENT_30][0] = m30;

fvals[WEIGHTED_SPAT_MOMENT_00][0] = wm00;
Expand All @@ -159,13 +197,22 @@ void ImageMomentsFeature::save_value(std::vector<std::vector<double>>& fvals)
fvals[WEIGHTED_SPAT_MOMENT_21][0] = wm21;
fvals[WEIGHTED_SPAT_MOMENT_30][0] = wm30;

fvals[CENTRAL_MOMENT_00][0] = mu00;
fvals[CENTRAL_MOMENT_01][0] = mu01;
fvals[CENTRAL_MOMENT_02][0] = mu02;
fvals[CENTRAL_MOMENT_03][0] = mu03;
fvals[CENTRAL_MOMENT_10][0] = mu10;
fvals[CENTRAL_MOMENT_11][0] = mu11;
fvals[CENTRAL_MOMENT_12][0] = mu12;
fvals[CENTRAL_MOMENT_13][0] = mu13;
fvals[CENTRAL_MOMENT_20][0] = mu20;
fvals[CENTRAL_MOMENT_21][0] = mu21;
fvals[CENTRAL_MOMENT_22][0] = mu22;
fvals[CENTRAL_MOMENT_23][0] = mu23;
fvals[CENTRAL_MOMENT_30][0] = mu30;
fvals[CENTRAL_MOMENT_31][0] = mu31;
fvals[CENTRAL_MOMENT_32][0] = mu32;
fvals[CENTRAL_MOMENT_33][0] = mu33;

fvals[WEIGHTED_CENTRAL_MOMENT_02][0] = wmu02;
fvals[WEIGHTED_CENTRAL_MOMENT_03][0] = wmu03;
Expand All @@ -188,8 +235,17 @@ void ImageMomentsFeature::save_value(std::vector<std::vector<double>>& fvals)
fvals[NORM_SPAT_MOMENT_02][0] = w02;
fvals[NORM_SPAT_MOMENT_03][0] = w03;
fvals[NORM_SPAT_MOMENT_10][0] = w10;
fvals[NORM_SPAT_MOMENT_11][0] = w11;
fvals[NORM_SPAT_MOMENT_12][0] = w12;
fvals[NORM_SPAT_MOMENT_13][0] = w13;
fvals[NORM_SPAT_MOMENT_20][0] = w20;
fvals[NORM_SPAT_MOMENT_21][0] = w21;
fvals[NORM_SPAT_MOMENT_22][0] = w22;
fvals[NORM_SPAT_MOMENT_23][0] = w23;
fvals[NORM_SPAT_MOMENT_30][0] = w30;
fvals[NORM_SPAT_MOMENT_31][0] = w31;
fvals[NORM_SPAT_MOMENT_32][0] = w32;
fvals[NORM_SPAT_MOMENT_33][0] = w33;

fvals[HU_M1][0] = hm1;
fvals[HU_M2][0] = hm2;
Expand Down Expand Up @@ -385,8 +441,11 @@ void ImageMomentsFeature::calcRawMoments (const pixcloud & cloud)
m10 = moment (cloud, 1, 0);
m11 = moment (cloud, 1, 1);
m12 = moment (cloud, 1, 2);
m13 = moment (cloud, 1, 3);
m20 = moment (cloud, 2, 0);
m21 = moment (cloud, 2, 1);
m22 = moment (cloud, 2, 2);
m23 = moment (cloud, 2, 3);
m30 = moment (cloud, 3, 0);
}

Expand Down Expand Up @@ -422,13 +481,25 @@ void ImageMomentsFeature::calcWeightedRawMoments (const pixcloud & cloud, const

void ImageMomentsFeature::calcCentralMoments (const pixcloud & cloud)
{
mu00 = centralMom (cloud, 0, 0);
mu01 = centralMom (cloud, 0, 1);
mu02 = centralMom (cloud, 0, 2);
mu03 = centralMom (cloud, 0, 3);

mu10 = centralMom (cloud, 1, 0);
mu11 = centralMom (cloud, 1, 1);
mu12 = centralMom (cloud, 1, 2);
mu13 = centralMom (cloud, 1, 3);

mu20 = centralMom (cloud, 2, 0);
mu21 = centralMom (cloud, 2, 1);
mu22 = centralMom (cloud, 2, 2);
mu23 = centralMom (cloud, 2, 3);

mu30 = centralMom (cloud, 3, 0);
mu31 = centralMom (cloud, 3, 1);
mu32 = centralMom (cloud, 3, 2);
mu33 = centralMom (cloud, 3, 3);
}

void ImageMomentsFeature::calcWeightedCentralMoments (const pixcloud & cloud)
Expand All @@ -442,8 +513,6 @@ void ImageMomentsFeature::calcWeightedCentralMoments (const pixcloud & cloud)
wmu30 = centralMom (cloud, 3, 0);
}

//

void ImageMomentsFeature::calcWeightedCentralMoments (const pixcloud& cloud, const intcloud& realintens)
{
wmu02 = centralMom (cloud, realintens, 0, 2);
Expand Down Expand Up @@ -472,9 +541,21 @@ void ImageMomentsFeature::calcNormRawMoments (const pixcloud & cloud)
w01 = normRawMom (cloud, 0, 1);
w02 = normRawMom (cloud, 0, 2);
w03 = normRawMom (cloud, 0, 3);

w10 = normRawMom (cloud, 1, 0);
w11 = normRawMom (cloud, 1, 1);
w12 = normRawMom (cloud, 1, 2);
w13 = normRawMom (cloud, 1, 3);

w20 = normRawMom (cloud, 2, 0);
w21 = normRawMom (cloud, 2, 1);
w22 = normRawMom (cloud, 2, 2);
w23 = normRawMom (cloud, 2, 3);

w30 = normRawMom (cloud, 3, 0);
w31 = normRawMom (cloud, 3, 1);
w32 = normRawMom (cloud, 3, 2);
w33 = normRawMom (cloud, 3, 3);
}

/// @brief Calculates the features for a subset of ROIs in a thread-safe way with other ROI subsets
Expand Down
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