diff --git a/src/TriangleMesh.cpp b/src/TriangleMesh.cpp
index 0cc768f79cb5a226c3bcd5227ef53cd02c65fc9f..a82653ef2bcf8d7398354022ad4545fe93a05fe6 100644
--- a/src/TriangleMesh.cpp
+++ b/src/TriangleMesh.cpp
@@ -1410,6 +1410,10 @@ void ActiveMesh::ScaleMesh(const Vector3F& scale)
filoMesh.fPoints[i].y*=scale.y;
filoMesh.fPoints[i].z*=scale.z;
}
+ for (unsigned int i=0; i< filoMesh.segFromRadius.size(); i++)
+ {
+ filoMesh.segFromRadius[i] *= 80.f;
+ }
}
}
@@ -1456,13 +1460,14 @@ void ActiveMesh::InitDots_body(const i3d::Image3d<i3d::GRAY16>& mask)
i3d::Image3d<float> perlinInner,perlinOutside;
perlinInner.CopyMetaData(mask);
- DoPerlin3D(perlinInner,5.0,0.8*1.5,0.7*1.5,6);
+// DoPerlin3D(perlinInner,5.0,0.8*1.5,0.7*1.5,6);
+ DoPerlin3D(perlinInner,1.0,0.8*1.3,0.7*1.5,6);
#ifdef SAVE_INTERMEDIATE_IMAGES
//perlinInner.SaveImage("2_PerlinAlone_Inner.ics");
#endif
perlinOutside.CopyMetaData(mask);
- DoPerlin3D(perlinOutside,1.8,0.8*1.5,0.7*1.5,6);
+ DoPerlin3D(perlinOutside,1.4,0.8*1.1,0.7*1.5,6);
#ifdef SAVE_INTERMEDIATE_IMAGES
//perlinOutside.SaveImage("2_PerlinAlone_Outside.ics");
#endif
@@ -1482,9 +1487,17 @@ void ActiveMesh::InitDots_body(const i3d::Image3d<i3d::GRAY16>& mask)
if (*p > 0.f)
{
//close to the surface?
- if (*p < 0.3f || *er == 0) *p=2000.f + 5000.f*(*pO); //corona
- else *p=600.f + 600.f*(*pI); //inside
- if (*er == 0) *p=2000.f; //std::max(*p,2000.f); //corona
+ if (*p < 0.2f || *er == 0)
+ *p=1000.f + 5000.f*(*pO); //corona
+ else if (*p < 0.4f)
+ {
+ float factor = (*p - 0.2f)/(0.2f);
+ *p=(300.f + 600.f*(*pI))*factor + (1000.f + 5000.f*(*pO))*(1.0f-factor);
+ }
+ else
+ *p=300.f + 600.f*(*pI); //inside
+
+ if (*er == 0) *p=1500.f; //corona
if (*p < 0.f) *p=0.f;
}
@@ -1551,8 +1564,8 @@ void ActiveMesh::InitDots_filo(const i3d::Image3d<i3d::GRAY16>& mask,const unsig
const float length=(tP-fP).Len(); //full segment has length = 0.005
//stepping along the axis
- const int S=(int)ceil(5.f*length/0.005); //"fraction factor"
- //std::cout << "S=" << S << ", length=" << length << "\n";
+ const int S=(int)ceil(5.f*length/0.005); //"fraction factor"\
+
for (int s=0; s < S; ++s)
{
//ratios "from" and "to"
@@ -1570,19 +1583,39 @@ void ActiveMesh::InitDots_filo(const i3d::Image3d<i3d::GRAY16>& mask,const unsig
p+=tS*tP;
//insert fl. dots
- r*=4000.f;
+ float dotsCount=400000.f*r;
+
+ // prevent data overflow (5 - multiplicity of addition)
+ int upper_limit = std::numeric_limits<i3d::GRAY16>::max() / (5 * TEXTURE_QUANTIZATION);
+ int qM=(dotsCount > upper_limit)? upper_limit : (int)dotsCount;
+
+ // establish 4 vectors - all orthogonal to the direction of filopodium
+ Vector3F mainDirection = tP-fP;
+ Vector3F vector1(-mainDirection.y, mainDirection.x, 0.0f);
+ Vector3F vector2(-vector1.x, -vector1.y, -vector1.z);
+
+ Vector3F vector3;
+ Mul(mainDirection, vector1, vector3);
- //std::cout << s << ": r=" << r << ", r*r=" << r*r << "\n";
+ Vector3F vector4;
+ Mul(mainDirection, vector2, vector4);
+
+ // make them as small as the size of the radius in the given position
+ vector1 *= r / vector1.Len();
+ vector2 *= r / vector2.Len();
+ vector3 *= r / vector3.Len();
+ vector4 *= r / vector4.Len();
- //float dotsCount=10.f*r*r;
- float dotsCount=100.f*r;
- int qM=(dotsCount > 1300.f)? 1300 : (int)dotsCount;
for (int q=0; q < qM; ++q)
{
dots_filo.push_back(p);
- dots_filo.push_back(p+Vector3F(0.0f,0.0f,+0.1f));
- dots_filo.push_back(p+Vector3F(0.0f,0.0f,-0.1f));
+ //dots_filo.push_back(p+Vector3F(0.0f,0.0f,+100*r));
+ //dots_filo.push_back(p+Vector3F(0.0f,0.0f,-100*r));
+ dots_filo.push_back(p+vector1);
+ dots_filo.push_back(p+vector2);
+ dots_filo.push_back(p+vector3);
+ dots_filo.push_back(p+vector4);
}
}
}
@@ -1897,10 +1930,6 @@ void ActiveMesh::PhaseII(const i3d::Image3d<i3d::GRAY16>& texture,
// convolution with real confocal PSF
i3d::Convolution<double>(fimg, psf, blurred_texture);
- // DEPRECATED - remove:
- // i3d::GaussIIR(intermediate,3.f,3.f,2.5f);
- // i3d::GaussIIR(intermediate,2.f,2.f,2.f);
-
#ifdef SAVE_INTERMEDIATE_IMAGES
blurred_texture.SaveImage("4_texture_blurred.ics");
#endif
@@ -1930,6 +1959,10 @@ void ActiveMesh::PhaseIII(i3d::Image3d<float>& blurred,
float* p=blurred.GetFirstVoxelAddr();
for (size_t i=0; i<blurred.GetImageSize(); i++, p++)
{
+ // shift the signal (simulates non-ideal black background)
+ // ?reflection of medium?
+ *p+=10.0f;
+
// PHOTON NOISE
// uncertainty in the number of incoming photons
// from statistics: shot noise = sqrt(signal)
@@ -1938,16 +1971,16 @@ void ActiveMesh::PhaseIII(i3d::Image3d<float>& blurred,
// for Poisson distribution E(X) = D(X)
const float noiseVar = noiseMean;
- *p+=30.f*((float)GetRandomPoisson(noiseMean) - noiseVar);
+ *p+=40.f*((float)GetRandomPoisson(noiseMean) - noiseVar);
- // DARK CURRENT NOISE
+ // DARK CURRENT
// constants are parameters of Andor iXon camera provided from vendor:
*p+=(float)GetRandomPoisson(0.06f);
// READOUT NOISE
// variance up to 25.f (old camera on ILBIT)
// variance about 1.f (for the new camera on ILBIT)
- *p+=GetRandomGauss(560.f,15.f);
+ *p+=GetRandomGauss(450.f,10.f);
}
#ifdef SAVE_INTERMEDIATE_IMAGES
blurred.SaveImage("6_texture_finalized.ics");