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feat: fixed deformation vector per soma and morphological closing [RQ-0304] #29

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58 changes: 58 additions & 0 deletions released_plugins/v3d_plugins/MIND/cellSegmentation_plugin.h
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Original file line number Diff line number Diff line change
Expand Up @@ -1091,6 +1091,64 @@ class cellSegmentation : public QObject {
ax2, ax3);
}

/**
* @brief Helper function to do 3D morphological closing on binary
* segmentation
*/
void morphologicalClosing3D(double *segmentation, V3DLONG cubeSize,
int kernelSize = 3) {
// Z axis (XY slices)
for (int z = 0; z < cubeSize; ++z) {
cv::Mat slice(cubeSize, cubeSize, CV_8UC1);
for (int y = 0; y < cubeSize; ++y)
for (int x = 0; x < cubeSize; ++x)
slice.at<uchar>(y, x) =
segmentation[z * cubeSize * cubeSize + y * cubeSize + x];
cv::Mat closed;
cv::morphologyEx(slice, closed, cv::MORPH_CLOSE,
cv::getStructuringElement(
cv::MORPH_RECT, cv::Size(kernelSize, kernelSize)));
for (int y = 0; y < cubeSize; ++y)
for (int x = 0; x < cubeSize; ++x)
segmentation[z * cubeSize * cubeSize + y * cubeSize + x] =
closed.at<uchar>(y, x);
}

// Y axis (XZ slices)
for (int y = 0; y < cubeSize; ++y) {
cv::Mat slice(cubeSize, cubeSize, CV_8UC1);
for (int z = 0; z < cubeSize; ++z)
for (int x = 0; x < cubeSize; ++x)
slice.at<uchar>(z, x) =
segmentation[z * cubeSize * cubeSize + y * cubeSize + x];
cv::Mat closed;
cv::morphologyEx(slice, closed, cv::MORPH_CLOSE,
cv::getStructuringElement(
cv::MORPH_RECT, cv::Size(kernelSize, kernelSize)));
for (int z = 0; z < cubeSize; ++z)
for (int x = 0; x < cubeSize; ++x)
segmentation[z * cubeSize * cubeSize + y * cubeSize + x] =
closed.at<uchar>(z, x);
}

// X axis (YZ slices)
for (int x = 0; x < cubeSize; ++x) {
cv::Mat slice(cubeSize, cubeSize, CV_8UC1);
for (int z = 0; z < cubeSize; ++z)
for (int y = 0; y < cubeSize; ++y)
slice.at<uchar>(z, y) =
segmentation[z * cubeSize * cubeSize + y * cubeSize + x];
cv::Mat closed;
cv::morphologyEx(slice, closed, cv::MORPH_CLOSE,
cv::getStructuringElement(
cv::MORPH_RECT, cv::Size(kernelSize, kernelSize)));
for (int z = 0; z < cubeSize; ++z)
for (int y = 0; y < cubeSize; ++y)
segmentation[z * cubeSize * cubeSize + y * cubeSize + x] =
closed.at<uchar>(z, y);
}
}

/**
* @brief Helper function to save the probabilistic model to a binary file.
*/
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46 changes: 26 additions & 20 deletions released_plugins/v3d_plugins/MIND/soma_simulation.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -991,6 +991,9 @@ void simulate_soma_data(V3DPluginCallback2 &callback, QWidget *parent) {
segMain.rotateSegmentation(tempIntensity, cubeSize, randomVec1, randomVec2,
randomVec3);

// Apply morphological closing to the synthetic segmentation
segMain.morphologicalClosing3D(tempSegmentation, cubeSize);

// Calculate intensity statistics from the extracted soma
double somaIntensitySum = 0.0;
double somaIntensityMin = 255.0;
Expand Down Expand Up @@ -1385,6 +1388,17 @@ void extractAndDeformSomaShape(
std::normal_distribution<double> normalDist(0.0, deformationStrength);
std::uniform_real_distribution<double> uniformDist(0.0, 1.0);

// Apply soma eigenvector-based deformation
double deformX = normalDist(gen) * somaEigenvector1[0] +
normalDist(gen) * somaEigenvector2[0] +
normalDist(gen) * somaEigenvector3[0];
double deformY = normalDist(gen) * somaEigenvector1[1] +
normalDist(gen) * somaEigenvector2[1] +
normalDist(gen) * somaEigenvector3[1];
double deformZ = normalDist(gen) * somaEigenvector1[2] +
normalDist(gen) * somaEigenvector2[2] +
normalDist(gen) * somaEigenvector3[2];

for (int z = 0; z < cubeSize; z++) {
for (int y = 0; y < cubeSize; y++) {
for (int x = 0; x < cubeSize; x++) {
Expand All @@ -1407,24 +1421,13 @@ void extractAndDeformSomaShape(
double distance =
sqrt(origX * origX + origY * origY + origZ * origZ);

// Apply soma eigenvector-based deformation
double deformX = normalDist(gen) * somaEigenvector1[0] +
normalDist(gen) * somaEigenvector2[0] +
normalDist(gen) * somaEigenvector3[0];
double deformY = normalDist(gen) * somaEigenvector1[1] +
normalDist(gen) * somaEigenvector2[1] +
normalDist(gen) * somaEigenvector3[1];
double deformZ = normalDist(gen) * somaEigenvector1[2] +
normalDist(gen) * somaEigenvector2[2] +
normalDist(gen) * somaEigenvector3[2];

// Scale deformation based on distance from center (less
// deformation at edges)
double radialFactor =
std::max(radialFactorMin, 1.0 - distance / radius);
deformX *= radialFactor;
deformY *= radialFactor;
deformZ *= radialFactor;
double scaledDeformX = deformX * radialFactor;
double scaledDeformY = deformY * radialFactor;
double scaledDeformZ = deformZ * radialFactor;

// Sample from probabilistic model to determine if this voxel
// should be kept, convert position to model coordinates
Expand All @@ -1450,12 +1453,15 @@ void extractAndDeformSomaShape(
// Keep voxel if probability is high enough
if (uniformDist(gen) < probability) {
// Apply deformation to final position
int finalX = static_cast<int>(std::round(origX + deformX)) +
cubeSize / 2;
int finalY = static_cast<int>(std::round(origY + deformY)) +
cubeSize / 2;
int finalZ = static_cast<int>(std::round(origZ + deformZ)) +
cubeSize / 2;
int finalX =
static_cast<int>(std::round(origX + scaledDeformX)) +
cubeSize / 2;
int finalY =
static_cast<int>(std::round(origY + scaledDeformY)) +
cubeSize / 2;
int finalZ =
static_cast<int>(std::round(origZ + scaledDeformZ)) +
cubeSize / 2;

// Check bounds and place in arrays
if (finalX >= 0 && finalX < cubeSize && finalY >= 0 &&
Expand Down
2 changes: 2 additions & 0 deletions released_plugins/v3d_plugins/MIND/soma_simulation.h
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,8 @@
#include <memory>
#include <random>
#include <vector>
#include <opencv2/imgproc.hpp>
#include <opencv2/core.hpp>

#include "basic_4dimage.h"
#include "cellSegmentation_plugin.h"
Expand Down