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POL3417 real-valued intensities for weighted moments (CPU) #146

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POL3417 real-valued intensities for weighted moments (CPU) #146

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67f65f5
real-valued intensities for weighted moments (non-GPU)
friskluft Sep 18, 2023
9532891
code cleaned
friskluft Sep 21, 2023
a90d1d2
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friskluft Sep 22, 2023
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13 changes: 11 additions & 2 deletions src/nyx/environment.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
#include "features/gldzm.h"
#include "features/glrlm.h"
#include "features/glszm.h"
#include "features/image_moments.h"
#include "features/ngldm.h"
#include "features/ngtdm.h"
#include "helpers/helpers.h"
Expand Down Expand Up @@ -61,7 +62,8 @@ namespace Nyxus
s_uppr == FEA_NICK_ALL_BUT_GABOR ||
s_uppr == FEA_NICK_ALL_BUT_GLCM ||
s_uppr == FEA_NICK_ALL_EASY ||
s_uppr == FEA_NICK_ALL_NEIG)
s_uppr == FEA_NICK_ALL_NEIG ||
s_uppr == FEA_NICK_2DMOMENTS)
{
result.push_back(s_uppr);
continue;
Expand Down Expand Up @@ -672,6 +674,12 @@ void Environment::process_feature_list()
break; // No need to bother of others
}

if (s == FEA_NICK_2DMOMENTS)
{
theFeatureSet.enableFeatures (ImageMomentsFeature::featureset);
continue;
}

// 's' is an individual feature name, not feature group name. Process it now
AvailableFeatures af;
if (! theFeatureSet.findFeatureByString(s, af))
Expand Down Expand Up @@ -1194,7 +1202,8 @@ void Environment::show_featureset_help()
FEA_NICK_ALL_NGTDM,
FEA_NICK_ALL_BUT_GABOR,
FEA_NICK_ALL_BUT_GLCM,
FEA_NICK_ALL_NEIG
FEA_NICK_ALL_NEIG,
FEA_NICK_2DMOMENTS
};

std::cout << "\n" <<
Expand Down
1 change: 1 addition & 0 deletions src/nyx/environment.h
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,7 @@
#define FEA_NICK_ALL_BUT_GLCM "*ALL_BUT_GLCM*"
#define FEA_NICK_ALL_EASY "*ALL_EASY*" // Equivalent to *ALL* minus GABOR, GLCM, and 2D moments
#define FEA_NICK_ALL_NEIG "*ALL_NEIGHBOR*"
#define FEA_NICK_2DMOMENTS "*2DMOMENTS*"

// Valid values of 'OUTPUTTYPE'
#define OT_SEPCSV "separatecsv"
Expand Down
201 changes: 161 additions & 40 deletions src/nyx/features/image_moments.cpp
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Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
#include "../environment.h"
#include "image_moments.h"

using pixelvector = std::vector<Pixel2>;

ImageMomentsFeature::ImageMomentsFeature() : FeatureMethod("ImageMomentsFeature")
{
provide_features({
Expand Down Expand Up @@ -88,35 +86,20 @@ void ImageMomentsFeature::calculate (LR& r)
calcHuInvariants (c);

// Prepare weighted pixel cloud
decltype(c) w = c;
apply_dist2contour_weighting (w, r.contour, weighting_epsilon);
std::vector<RealPixIntens> w;
Nyxus::copy_pixcloud_intensities (w, c);
Nyxus::apply_dist2contour_weighting (w, c, r.contour, weighting_epsilon);

// Calculate weighted moments
calcOrigins (w);
calcWeightedRawMoments (w);
calcWeightedCentralMoments (w);
calcWeightedHuInvariants (w);
calcOrigins (c, w);
calcWeightedRawMoments (c, w);
calcWeightedCentralMoments (c, w);
calcWeightedHuInvariants (c, w);
}

#ifdef USE_GPU
void ImageMomentsFeature::calculate_via_gpu (LR& r, size_t roi_idx)
{
//ImageMatrix& im = r.aux_image_matrix;
//
//bool ok = ImageMomentsFeature_calculate2(
// m00, m01, m02, m03, m10, m11, m12, m20, m21, m30, // spatial moments
// mu02, mu03, mu11, mu12, mu20, mu21, mu30, // central moments
// nu02, nu03, nu11, nu12, nu20, nu21, nu30, // normalized central moments
// w00, w01, w02, w03, w10, w20, w30, // 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
// whm1, whm2, whm3, whm4, whm5, whm6, whm7, // weighted Hum moments
// im,
// roi_idx,
// r.aabb.get_xmin(),
// r.aabb.get_ymin());

bool ok = ImageMomentsFeature_calculate3(
m00, m01, m02, m03, m10, m11, m12, m20, m21, m30, // spatial moments
mu02, mu03, mu11, mu12, mu20, mu21, mu30, // central moments
Expand Down Expand Up @@ -215,7 +198,7 @@ void ImageMomentsFeature::save_value(std::vector<std::vector<double>>& fvals)
fvals[WEIGHTED_HU_M7][0] = whm7;
}

/// @brief Calculates the spatial 2D moment of order q,p f ROI pixel cloud
/// @brief Calculates a spatial 2D moment of order q,p of ROI pixel cloud
double ImageMomentsFeature::moment (const pixcloud& cloud, int p, int q)
{
double q_ = q, p_ = p, sum = 0;
Expand All @@ -224,24 +207,57 @@ double ImageMomentsFeature::moment (const pixcloud& cloud, int p, int q)
return sum;
}

void ImageMomentsFeature::calcOrigins (const std::vector<Pixel2>& cloud)
/// @brief Calculates a spatial 2D moment of order q,p of ROI pixel cloud 'c' using real-valued intensities 'real_intens'
double ImageMomentsFeature::moment (const pixcloud & c, const intcloud & real_intens, int p, int q)
{
double q_ = q, p_ = p, sum = 0;
size_t n = c.size();
for (size_t i=0; i<n; i++)
{
const Pixel2& pxl = c[i];
sum += real_intens[i] * pow(double(pxl.x - baseX), p_) * pow(double(pxl.y - baseY), q_);
}
return sum;
}

void ImageMomentsFeature::calcOrigins (const pixcloud & cloud)
{
double m00 = moment (cloud, 0, 0);
originOfX = moment (cloud, 1, 0) / m00;
originOfY = moment (cloud, 0, 1) / m00;
}

void ImageMomentsFeature::calcOrigins (const pixcloud & cloud, const intcloud & real_valued_intensities)
{
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double m00 = moment (cloud, real_valued_intensities, 0, 0);
originOfX = moment (cloud, real_valued_intensities, 1, 0) / m00;
originOfY = moment (cloud, real_valued_intensities, 0, 1) / m00;
}

/// @brief Calculates the central 2D moment of order q,p of ROI pixel cloud
double ImageMomentsFeature::centralMom (const std::vector<Pixel2>& cloud, int p, int q)
double ImageMomentsFeature::centralMom (const pixcloud & cloud, int p, int q)
{
double sum = 0;
for (auto& pxl : cloud)
sum += double(pxl.inten) * pow(double(pxl.x-baseX) - originOfX, p) * pow(double(pxl.y-baseY) - originOfY, q);
return sum;
}

/// @brief Calculates the central 2D moment of order q,p of ROI pixel cloud using real-valued intensities
double ImageMomentsFeature::centralMom (const pixcloud & cloud, const intcloud & realintens, int p, int q)
{
double sum = 0;
size_t n = cloud.size();
for (size_t i = 0; i < n; i++)
{
auto& pxl = cloud[i];
sum += realintens[i] * pow(double(pxl.x - baseX) - originOfX, p) * pow(double(pxl.y - baseY) - originOfY, q);
}
return sum;
}

/// @brief Calculates the normalized spatial 2D moment of order q,p of ROI pixel cloud
double ImageMomentsFeature::normRawMom (const std::vector <Pixel2>& cloud, int p, int q)
double ImageMomentsFeature::normRawMom (const pixcloud & cloud, int p, int q)
{
double stddev = centralMom (cloud, 2, 2);
int w = std::max(q, p);
Expand All @@ -252,14 +268,22 @@ double ImageMomentsFeature::normRawMom (const std::vector <Pixel2>& cloud, int p
}

/// @brief Calculates the normalized central 2D moment of order q,p of ROI pixel cloud
double ImageMomentsFeature::normCentralMom (const std::vector<Pixel2>& cloud, int p, int q)
double ImageMomentsFeature::normCentralMom (const pixcloud & cloud, int p, int q)
{
double temp = ((double(p) + double(q)) / 2.0) + 1.0;
double retval = centralMom(cloud, p, q) / pow(moment (cloud, 0, 0), temp);
return retval;
}

std::tuple<double, double, double, double, double, double, double> ImageMomentsFeature::calcHuInvariants_imp (const std::vector<Pixel2>& cloud)
/// @brief Calculates the normalized central 2D moment of order q,p of ROI pixel cloud using real-valued intensities 'realintens'
double ImageMomentsFeature::normCentralMom (const pixcloud & cloud, const intcloud & realintens, int p, int q)
{
double temp = ((double(p) + double(q)) / 2.0) + 1.0;
double retval = centralMom(cloud, realintens, p, q) / pow(moment(cloud, realintens, 0, 0), temp);
return retval;
}

std::tuple<double, double, double, double, double, double, double> ImageMomentsFeature::calcHuInvariants_imp (const pixcloud & cloud)
{
// calculate the 7 Hu-1962 invariants

Expand Down Expand Up @@ -292,17 +316,55 @@ std::tuple<double, double, double, double, double, double, double> ImageMomentsF
return { h1, h2, h3, h4, h5, h6, h7 };
}

void ImageMomentsFeature::calcHuInvariants (const std::vector<Pixel2>& cloud)
std::tuple<double, double, double, double, double, double, double> ImageMomentsFeature::calcHuInvariants_imp (const pixcloud & cloud, const intcloud & realintens)
{
// calculate the 7 Hu-1962 invariants

auto _20 = normCentralMom (cloud, realintens, 2, 0),
_02 = normCentralMom (cloud, realintens, 0, 2),
_11 = normCentralMom (cloud, realintens, 1, 1),
_30 = normCentralMom (cloud, realintens, 3, 0),
_12 = normCentralMom (cloud, realintens, 1, 2),
_21 = normCentralMom (cloud, realintens, 2, 1),
_03 = normCentralMom (cloud, realintens, 0, 3);

double h1 = _20 + _02;
double h2 = pow((_20 - _02), 2) + 4 * (pow(_11, 2));
double h3 = pow((_30 - 3 * _12), 2) +
pow((3 * _21 - _03), 2);
double h4 = pow((_30 + _12), 2) +
pow((_21 + _03), 2);
double h5 = (_30 - 3 * _12) *
(_30 + _12) *
(pow(_30 + _12, 2) - 3 * pow(_21 + _03, 2)) +
(3 * _21 - _03) * (_21 + _03) *
(pow(3 * (_30 + _12), 2) - pow(_21 + _03, 2));
double h6 = (_20 - _02) * (pow(_30 + _12, 2) -
pow(_21 + _03, 2)) + (4 * _11 * (_30 + _12) *
_21 + _03);
double h7 = (3 * _21 - _03) * (_30 + _12) * (pow(_30 + _12, 2) -
3 * pow(_21 + _03, 2)) - (_30 - 3 * _12) * (_21 + _03) *
(3 * pow(_30 + _12, 2) - pow(_21 + _03, 2));

return { h1, h2, h3, h4, h5, h6, h7 };
}

void ImageMomentsFeature::calcHuInvariants (const pixcloud & cloud)
{
std::tie(hm1, hm2, hm3, hm4, hm5, hm6, hm7) = calcHuInvariants_imp (cloud);
}

void ImageMomentsFeature::calcWeightedHuInvariants (const std::vector<Pixel2>& cloud)
void ImageMomentsFeature::calcWeightedHuInvariants (const pixcloud & cloud)
{
std::tie(whm1, whm2, whm3, whm4, whm5, whm6, whm7) = calcHuInvariants_imp (cloud);
}

void ImageMomentsFeature::calcRawMoments (const std::vector<Pixel2>& cloud)
void ImageMomentsFeature::calcWeightedHuInvariants (const pixcloud & cloud, const intcloud & realintens)
{
std::tie(whm1, whm2, whm3, whm4, whm5, whm6, whm7) = calcHuInvariants_imp (cloud, realintens);
}

void ImageMomentsFeature::calcRawMoments (const pixcloud & cloud)
{
m00 = moment (cloud, 0, 0);
m01 = moment (cloud, 0, 1);
Expand All @@ -318,7 +380,7 @@ void ImageMomentsFeature::calcRawMoments (const std::vector<Pixel2>& cloud)

/// @brief
/// @param cloud Cloud of weighted ROI pixels
void ImageMomentsFeature::calcWeightedRawMoments (const std::vector<Pixel2>& cloud)
void ImageMomentsFeature::calcWeightedRawMoments (const pixcloud & cloud)
{
wm00 = moment (cloud, 0, 0);
wm01 = moment (cloud, 0, 1);
Expand All @@ -332,7 +394,21 @@ void ImageMomentsFeature::calcWeightedRawMoments (const std::vector<Pixel2>& clo
wm30 = moment (cloud, 3, 0);
}

void ImageMomentsFeature::calcCentralMoments (const std::vector<Pixel2>& cloud)
void ImageMomentsFeature::calcWeightedRawMoments (const pixcloud & cloud, const intcloud & real_intens)
{
wm00 = moment (cloud, real_intens, 0, 0);
wm01 = moment (cloud, real_intens, 0, 1);
wm02 = moment (cloud, real_intens, 0, 2);
wm03 = moment (cloud, real_intens, 0, 3);
wm10 = moment (cloud, real_intens, 1, 0);
wm11 = moment (cloud, real_intens, 1, 1);
wm12 = moment (cloud, real_intens, 1, 2);
wm20 = moment (cloud, real_intens, 2, 0);
wm21 = moment (cloud, real_intens, 2, 1);
wm30 = moment (cloud, real_intens, 3, 0);
}

void ImageMomentsFeature::calcCentralMoments (const pixcloud & cloud)
{
mu02 = centralMom (cloud, 0, 2);
mu03 = centralMom (cloud, 0, 3);
Expand All @@ -343,7 +419,7 @@ void ImageMomentsFeature::calcCentralMoments (const std::vector<Pixel2>& cloud)
mu30 = centralMom (cloud, 3, 0);
}

void ImageMomentsFeature::calcWeightedCentralMoments (const std::vector<Pixel2>& cloud)
void ImageMomentsFeature::calcWeightedCentralMoments (const pixcloud & cloud)
{
wmu02 = centralMom (cloud, 0, 2);
wmu03 = centralMom (cloud, 0, 3);
Expand All @@ -354,7 +430,20 @@ void ImageMomentsFeature::calcWeightedCentralMoments (const std::vector<Pixel2>&
wmu30 = centralMom (cloud, 3, 0);
}

void ImageMomentsFeature::calcNormCentralMoments (const std::vector<Pixel2>& cloud)
//

void ImageMomentsFeature::calcWeightedCentralMoments (const pixcloud& cloud, const intcloud& realintens)
{
wmu02 = centralMom (cloud, realintens, 0, 2);
wmu03 = centralMom (cloud, realintens, 0, 3);
wmu11 = centralMom (cloud, realintens, 1, 1);
wmu12 = centralMom (cloud, realintens, 1, 2);
wmu20 = centralMom (cloud, realintens, 2, 0);
wmu21 = centralMom (cloud, realintens, 2, 1);
wmu30 = centralMom (cloud, realintens, 3, 0);
}

void ImageMomentsFeature::calcNormCentralMoments (const pixcloud & cloud)
{
nu02 = normCentralMom (cloud, 0, 2);
nu03 = normCentralMom (cloud, 0, 3);
Expand All @@ -365,7 +454,7 @@ void ImageMomentsFeature::calcNormCentralMoments (const std::vector<Pixel2>& clo
nu30 = normCentralMom (cloud, 3, 0);
}

void ImageMomentsFeature::calcNormRawMoments (const std::vector<Pixel2>& cloud)
void ImageMomentsFeature::calcNormRawMoments (const pixcloud & cloud)
{
w00 = normRawMom (cloud, 0, 0);
w01 = normRawMom (cloud, 0, 1);
Expand Down Expand Up @@ -403,8 +492,8 @@ void ImageMomentsFeature::parallel_process_1_batch (size_t start, size_t end, st
/// @param ptrLabelData ROI data
void ImageMomentsFeature::gpu_process_all_rois (const std::vector<int> & Labels, std::unordered_map <int, LR>& RoiData)
{
// Send image matrices to GPU-side
bool ok = send_imgmatrices_to_gpu (ImageMatrixBuffer, imageMatrixBufferLen);
// Transfers a solid buffer of whole image's combined image matrices to GPU-side
bool ok = send_imgmatrices_to_gpu (Nyxus::ImageMatrixBuffer, Nyxus::imageMatrixBufferLen, Nyxus::largest_roi_imatr_buf_len);

// Prepare consolidated all-ROI contours for pixel weighting in weighted moments
std::vector<size_t> hoIndices;
Expand Down Expand Up @@ -445,3 +534,35 @@ void ImageMomentsFeature::gpu_process_all_rois (const std::vector<int> & Labels,
}
#endif

namespace Nyxus
{
void copy_pixcloud_intensities (intcloud & dst, const pixcloud & src)
{
dst.reserve (src.size());
for (auto pxl : src)
dst.push_back (RealPixIntens(pxl.inten));
}

/// @brief Applies to distance-to-contour weighting to intensities of pixel cloud. Saves the result in 'realintens'
void apply_dist2contour_weighting(
// input & output
intcloud & realintens,
// input
const pixcloud & cloud,
const pixcloud & contour,
const double epsilon)
{
size_t n = cloud.size();
for (size_t i = 0; i < n; i++)
{
auto& p = cloud[i];

// pixel distance
auto mind2 = p.min_sqdist(contour);
double dist = std::sqrt(mind2);

// weighted intensity
realintens[i] = double(p.inten) / (dist + epsilon);
}
}
}
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