From 19a7f90ea832b2a4865a23f7359f083a44d92587 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vladim=C3=ADr=20Ulman?= <ulman@mpi-cbg.de>
Date: Sun, 8 Jan 2017 09:31:18 +0100
Subject: [PATCH] Moved filopodia geometry meta-data (fPoints, segFromPoints
etc.) into the mesh_t structure, so now every filopodium remembers it. This
is useful for generating filo texture later. Mesh moving and scaling
functions were updated to reflect this.
Updated ImportVTK_Ftree() and InitDots_filo() so that the former really only
reads the filo geometry and the latter creates a texture for it.
Filopodia skeleton segments are displayed in OpenGL now by default.
---
cmath3d/TriangleMesh.cpp | 203 +++++++++++++++++++--------------------
cmath3d/TriangleMesh.h | 15 ++-
src/graphics.cpp | 38 ++++----
src/main.cpp | 18 +++-
4 files changed, 138 insertions(+), 136 deletions(-)
diff --git a/cmath3d/TriangleMesh.cpp b/cmath3d/TriangleMesh.cpp
index 9df2d59..e7193c7 100644
--- a/cmath3d/TriangleMesh.cpp
+++ b/cmath3d/TriangleMesh.cpp
@@ -490,10 +490,10 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
//local/temporary list of vertices of segments that make up the f-tree
//later, we convert these to triangles and save these guys instead
- fPoints.clear();
- segFromPoint.clear();
- segToPoint.clear();
- segFromRadius.clear();
+ filoMesh.fPoints.clear();
+ filoMesh.segFromPoint.clear();
+ filoMesh.segToPoint.clear();
+ filoMesh.segFromRadius.clear();
//try to open the file
std::ifstream file(filename);
@@ -546,7 +546,7 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
file.ignore(10240,'\n');
//std::cout << "reading " << itemCount << " point coordinates\n";
- fPoints.reserve(itemCount);
+ filoMesh.fPoints.reserve(itemCount);
//read all points...
float x,y,z;
@@ -557,7 +557,7 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
//... and save them
Vector3FC v1(x,y,z);
//v1*=100.f;
- fPoints.push_back(v1);
+ filoMesh.fPoints.push_back(v1);
--itemCount;
}
@@ -573,9 +573,9 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
file.ignore(10240,'\n');
//std::cout << "reading " << itemCount << " segments\n";
- segFromPoint.reserve(itemCount);
- segToPoint.reserve(itemCount);
- segFromRadius.reserve(itemCount);
+ filoMesh.segFromPoint.reserve(itemCount);
+ filoMesh.segToPoint.reserve(itemCount);
+ filoMesh.segFromRadius.reserve(itemCount);
//read all segments vertices
int ignore,v1,v2;
@@ -583,8 +583,8 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
{
file >> v1 >> v2;
- segFromPoint.push_back(v1);
- segToPoint.push_back(v2);
+ filoMesh.segFromPoint.push_back(v1);
+ filoMesh.segToPoint.push_back(v2);
--itemCount;
}
@@ -623,7 +623,7 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
v1=0;
while (itemCount > 0 && file >> x)
{
- segFromRadius.push_back(x*radiusCorrection);
+ filoMesh.segFromRadius.push_back(x*radiusCorrection);
--itemCount;
++v1;
@@ -639,17 +639,16 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
//we need to render the circular-like base (as triangle fan),
//and the cylinder-like "cone" towards the tip; this point is for the triangle fan
const size_t fanCentrePoint=filoMesh.Pos.size();
- filoMesh.Pos.push_back(fPoints[segFromPoint[0]]);
+ filoMesh.Pos.push_back(filoMesh.fPoints[filoMesh.segFromPoint[0]]);
//bookmark the beginning of the cylinder-like surface points
size_t firstRadiusPoint=filoMesh.Pos.size();
- PointsFirstOffset=firstRadiusPoint;
//will store a former nXaxis
Vector3F pXaxis;
//for all bending points except the last one (tip)
- for (unsigned int i=0; i < segFromPoint.size(); ++i)
+ for (unsigned int i=0; i < filoMesh.segFromPoint.size(); ++i)
{
//we need to construct rotation matrix that would
//rotate points on a circle which lays in the XZ plane
@@ -658,11 +657,11 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
//would be normal
//
//new Y axis
- Vector3F nYaxis=fPoints[segToPoint[i]];
- if (i == 0) nYaxis-=fPoints[segFromPoint[i]];
+ Vector3F nYaxis=filoMesh.fPoints[filoMesh.segToPoint[i]];
+ if (i == 0) nYaxis-=filoMesh.fPoints[filoMesh.segFromPoint[i]];
else
{
- nYaxis-=fPoints[segFromPoint[i-1]];
+ nYaxis-=filoMesh.fPoints[filoMesh.segFromPoint[i-1]];
nYaxis/=2.f; //unnecessary scaling
}
@@ -709,21 +708,21 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
for (int p=0; p < PointsOnRadiusPeriphery; ++p)
{
//the point in its original position
- float x=segFromRadius[i]*cosf(6.28f*float(p)/float(PointsOnRadiusPeriphery));
- float z=segFromRadius[i]*sinf(6.28f*float(p)/float(PointsOnRadiusPeriphery));
+ float x=filoMesh.segFromRadius[i]*cosf(6.28f*float(p)/float(PointsOnRadiusPeriphery));
+ float z=filoMesh.segFromRadius[i]*sinf(6.28f*float(p)/float(PointsOnRadiusPeriphery));
//rotate
Vector3FC V(x*nXaxis);
V+=z*nZaxis;
//shift to the centre and save
- V+=fPoints[segFromPoint[i]];
+ V+=filoMesh.fPoints[filoMesh.segFromPoint[i]];
filoMesh.Pos.push_back(V);
}
}
//finally, add the tip point
- filoMesh.Pos.push_back(fPoints[segToPoint.back()]);
+ filoMesh.Pos.push_back(filoMesh.fPoints[filoMesh.segToPoint.back()]);
//now, add the triangle fan - aka filopodia base
for (size_t p=0; p < PointsOnRadiusPeriphery-1; ++p)
@@ -740,7 +739,7 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
//now create triangles for all segment strips
//except the last one (that leads to the tip)
- for (unsigned int i=1; i < segFromPoint.size(); ++i)
+ for (unsigned int i=1; i < filoMesh.segFromPoint.size(); ++i)
{
int p=0;
for (; p < PointsOnRadiusPeriphery-1; ++p)
@@ -784,63 +783,6 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
filoMesh.ID.push_back(firstRadiusPoint+PointsOnRadiusPeriphery);
filoMesh.norm.push_back(fictiveNormal);
- //render the filopodium texture points along its skeleton
- //the amount of points is determined from the radius, from circle area -> square of radius
- for (size_t i=0; i < segFromPoint.size(); ++i)
- {
- //time-savers...
- const Vector3F& fP=fPoints[segFromPoint[i]];
- const Vector3F& tP=fPoints[segToPoint[i]];
-
- 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";
- for (int s=0; s < S; ++s)
- {
- //ratios "from" and "to"
- const float fS=float(S-s)/float(S);
- const float tS=float(s)/float(S);
-
- //target radius
- const float target_r=(i+1 < segFromPoint.size())? segFromRadius[i+1] : 0.f;
-
- //current radius
- float r=fS*segFromRadius[i] + tS*target_r;
-
- //current position
- Vector3F p =fS*fP;
- p+=tS*tP;
-
- //modify coordinates exactly the same as mesh coordinates will be modified
- //TODO: devise a universal function to shift points to target place
- //and make all function use this one, so that shift must be changed at only place!
- p.x*=180.f;
- p.y*=180.f;
- p.z*=250.f;
- p.x+=13.75f;
- p.y+=13.75f;
- p.z+=11.00f;
-
- //insert fl. dots
- r*=4000.f;
-
- //std::cout << s << ": r=" << r << ", r*r=" << r*r << "\n";
-
- //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));
- }
- }
- }
-
return(0);
}
@@ -1057,7 +999,7 @@ void ActiveMesh::RenderMask_filo(i3d::Image3d<i3d::GRAY16>& mask,const int idx,c
i3d::FloodFill(tmpI,(i3d::GRAY16)50,0);
//this removes the flooding while filling
- //everything else (and closing holes in this was)
+ //everything else (and closing holes in this way)
i3d::GRAY16* pI=tmpI.GetFirstVoxelAddr();
i3d::GRAY16* pM=mask.GetFirstVoxelAddr();
i3d::GRAY16* const pL=pM+mask.GetImageSize();
@@ -1196,17 +1138,30 @@ void ActiveMesh::CenterMesh(const Vector3F& newCentre)
z-=newCentre.z;
//shift the centre to point (0,0,0)
+ //cell body
for (unsigned int i=0; i < Pos.size(); ++i)
{
Pos[i].x-=float(x);
Pos[i].y-=float(y);
Pos[i].z-=float(z);
}
- for (unsigned int i=0; i < fPoints.size(); ++i)
+
+ //filopodia
+ for (unsigned int f=0; f < Ftree.size(); ++f)
{
- fPoints[i].x-=float(x);
- fPoints[i].y-=float(y);
- fPoints[i].z-=float(z);
+ mesh_t& filoMesh=Ftree[f];
+ for (unsigned int i=0; i < filoMesh.Pos.size(); ++i)
+ {
+ filoMesh.Pos[i].x-=float(x);
+ filoMesh.Pos[i].y-=float(y);
+ filoMesh.Pos[i].z-=float(z);
+ }
+ for (unsigned int i=0; i < filoMesh.fPoints.size(); ++i)
+ {
+ filoMesh.fPoints[i].x-=float(x);
+ filoMesh.fPoints[i].y-=float(y);
+ filoMesh.fPoints[i].z-=float(z);
+ }
}
}
@@ -1231,6 +1186,12 @@ void ActiveMesh::ScaleMesh(const Vector3F& scale)
filoMesh.Pos[i].y*=scale.y;
filoMesh.Pos[i].z*=scale.z;
}
+ for (unsigned int i=0; i < filoMesh.fPoints.size(); ++i)
+ {
+ filoMesh.fPoints[i].x*=scale.x;
+ filoMesh.fPoints[i].y*=scale.y;
+ filoMesh.fPoints[i].z*=scale.z;
+ }
}
}
@@ -1255,6 +1216,12 @@ void ActiveMesh::TranslateMesh(const Vector3F& shift)
filoMesh.Pos[i].y+=shift.y;
filoMesh.Pos[i].z+=shift.z;
}
+ for (unsigned int i=0; i < filoMesh.fPoints.size(); ++i)
+ {
+ filoMesh.fPoints[i].x+=shift.x;
+ filoMesh.fPoints[i].y+=shift.y;
+ filoMesh.fPoints[i].z+=shift.z;
+ }
}
}
@@ -1564,28 +1531,56 @@ void ActiveMesh::InitDots_body(const i3d::Image3d<i3d::GRAY16>& mask)
//#endif
}
-void ActiveMesh::InitDots_filo(const i3d::Image3d<i3d::GRAY16>& mask)
+void ActiveMesh::InitDots_filo(const i3d::Image3d<i3d::GRAY16>& mask,const int idx)
{
- //time savers...
- const float xRes=mask.GetResolution().GetX();
- const float yRes=mask.GetResolution().GetY();
- const float zRes=mask.GetResolution().GetZ();
- const float xOff=mask.GetOffset().x;
- const float yOff=mask.GetOffset().y;
- const float zOff=mask.GetOffset().z;
+ //syntactic short-cut to the proper filopodium geometry data
+ mesh_t& filoMesh=Ftree[idx];
- const i3d::GRAY16* p=mask.GetFirstVoxelAddr();
- for (int z=0; z < (signed)mask.GetSizeZ(); ++z)
- for (int y=0; y < (signed)mask.GetSizeY(); ++y)
- for (int x=0; x < (signed)mask.GetSizeX(); ++x, ++p)
- if (*p > 100)
+ //render the filopodium texture points along its skeleton
+ //the amount of points is determined from the radius, from circle area -> square of radius
+ for (size_t i=0; i < filoMesh.segFromPoint.size(); ++i)
{
- //convert px coords into um
- const float X=(float)x/xRes + xOff;
- const float Y=(float)y/yRes + yOff;
- const float Z=(float)z/zRes + zOff;
+ //time-savers...
+ const Vector3F& fP=filoMesh.fPoints[filoMesh.segFromPoint[i]];
+ const Vector3F& tP=filoMesh.fPoints[filoMesh.segToPoint[i]];
+
+ 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";
+ for (int s=0; s < S; ++s)
+ {
+ //ratios "from" and "to"
+ const float fS=float(S-s)/float(S);
+ const float tS=float(s)/float(S);
- for (int q=0; q < 80; ++q) dots.push_back(Vector3F(X,Y,Z));
+ //target radius
+ const float target_r=(i+1 < filoMesh.segFromPoint.size())? filoMesh.segFromRadius[i+1] : 0.f;
+
+ //current radius
+ float r=fS*filoMesh.segFromRadius[i] + tS*target_r;
+
+ //current position
+ Vector3F p =fS*fP;
+ p+=tS*tP;
+
+ //insert fl. dots
+ r*=4000.f;
+
+ //std::cout << s << ": r=" << r << ", r*r=" << r*r << "\n";
+
+ //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));
+ }
+ }
}
}
@@ -1593,8 +1588,10 @@ void ActiveMesh::InitDots_filo(const i3d::Image3d<i3d::GRAY16>& mask)
void ActiveMesh::BrownDots(const i3d::Image3d<i3d::GRAY16>& mask)
{
//TODO REMOVE ME
+ /*
for (size_t i=0; i < dots.size(); ++i)
dots[i].x+=1.0f;
+ */
}
diff --git a/cmath3d/TriangleMesh.h b/cmath3d/TriangleMesh.h
index a466e4b..1741ae0 100644
--- a/cmath3d/TriangleMesh.h
+++ b/cmath3d/TriangleMesh.h
@@ -10,6 +10,12 @@ struct mesh_t {
std::vector<long unsigned int> ID; //list of triangles organized in tripplets of indices into the Pos array of vertices;
//the array length should be 3x the number of triangles in the mesh
std::vector<Vector3F> norm; //list of vectors that are normal/orthogonal to the planes given by the individual triangles
+
+ ///metadata to keep the skeleton information
+ std::vector<Vector3FC> fPoints; //skel. vertex coordinates
+ std::vector<int> segFromPoint; //indices of starting points of all segments
+ std::vector<int> segToPoint; //...of ending points
+ std::vector<float> segFromRadius; //radii at starting points for all segments
};
/**
@@ -125,13 +131,6 @@ class ActiveMesh
int ImportVTK_Volumetric(const char* filename,bool saveAlsoTetrahedra=false);
int ImportVTK_Ftree(const char* filename,const int idx,const float stretch=1.f,bool resetMesh=true);
- std::vector<Vector3FC> fPoints;
- std::vector<int> segFromPoint; //segment description, quite ugly solution for now
- std::vector<int> segToPoint;
- std::vector<float> segFromRadius;
- std::vector<float> segToRadius;
- size_t PointsFirstOffset;
-
///naive, but it works
//renders first aside, then overlays the given mask
void RenderMask_body(i3d::Image3d<i3d::GRAY16>& mask,const bool showTriangles=false);
@@ -146,7 +145,7 @@ class ActiveMesh
///time-lapse (coherent) manipulation with fluorescent dots,
///always with the given mask
void InitDots_body(const i3d::Image3d<i3d::GRAY16>& mask);
- void InitDots_filo(const i3d::Image3d<i3d::GRAY16>& mask); //TODO: if it would work, keep skeleton of every filopodium and introduce points accordingly
+ void InitDots_filo(const i3d::Image3d<i3d::GRAY16>& mask,const int idx);
void BrownDots(const i3d::Image3d<i3d::GRAY16>& mask);
void FFDots(const i3d::Image3d<i3d::GRAY16>& mask,
diff --git a/src/graphics.cpp b/src/graphics.cpp
index 684fdf6..6ba1df6 100644
--- a/src/graphics.cpp
+++ b/src/graphics.cpp
@@ -356,32 +356,28 @@ void ActiveMesh::displayMesh(void)
glEnd();
}
-/*
- //show line segments
- glLineWidth(1);
+/**/
+ //show filopodia line segments
+ glLineWidth(4);
glBegin(GL_LINES);
- for (unsigned int i=0; i < segFromPoint.size(); ++i)
+ for (size_t f=0; f < Ftree.size(); ++f)
{
- glVertex3f(fPoints[segFromPoint[i]].x,
- fPoints[segFromPoint[i]].y,
- fPoints[segFromPoint[i]].z);
- glVertex3f(fPoints[segToPoint[i]].x,
- fPoints[segToPoint[i]].y,
- fPoints[segToPoint[i]].z);
+ mesh_t& filoMesh=Ftree[f];
+ for (unsigned int i=0; i < filoMesh.segFromPoint.size(); ++i)
+ {
+ glVertex3f(filoMesh.fPoints[filoMesh.segFromPoint[i]].x,
+ filoMesh.fPoints[filoMesh.segFromPoint[i]].y,
+ filoMesh.fPoints[filoMesh.segFromPoint[i]].z);
+ glVertex3f(filoMesh.fPoints[filoMesh.segToPoint[i]].x,
+ filoMesh.fPoints[filoMesh.segToPoint[i]].y,
+ filoMesh.fPoints[filoMesh.segToPoint[i]].z);
+ }
}
glEnd();
+ glLineWidth(1);
+/**/
- //show points after rotation
- glPointSize(3);
- glBegin(GL_POINTS);
- for (unsigned int i=0; i < 10*segFromPoint.size()+1; ++i)
- glVertex3f(Pos[PointsFirstOffset+i].x,
- Pos[PointsFirstOffset+i].y,
- Pos[PointsFirstOffset+i].z);
- glEnd();
-*/
-
- //display filopodias
+ //display filopodia
for (size_t f=0; f < Ftree.size(); ++f)
{
int color=f%2;
diff --git a/src/main.cpp b/src/main.cpp
index dca2504..adab43e 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -192,8 +192,6 @@ int LoadNewMesh(int fileNo)
return(1);
}
- mesh.dots_filo.clear();
- mesh.dots_filo.reserve(300000);
retval=mesh.ImportVTK_Ftree(VTK_fTreeA,0);
if (retval)
{
@@ -244,7 +242,12 @@ int RenderMesh(int fileNo)
{
std::cout << "rendering texture first run\n";
mesh.InitDots_body(mask);
- //mesh.InitDots_filo(mask); -- already re-created with ImportVTK_Ftree()
+
+ //second, create texture for filopodia
+ mesh.dots_filo.clear();
+ mesh.dots_filo.reserve(300000);
+ mesh.InitDots_filo(mask,0); //filopodium one by one
+ mesh.InitDots_filo(mask,1);
std::cout << "filo dots size=" << mesh.dots_filo.size() << "\n";
}
else
@@ -290,7 +293,14 @@ int RenderMesh(int fileNo)
//apply the FF on the fl. dots
mesh.FFDots(mask,FF);
- //FF destructor will delete dyn. allocated images...
+ //FF destructor will delete dyn. allocated images in the FF...
+
+ //also update filopodia (by re-creating them from the scratch)
+ mesh.dots_filo.clear();
+ mesh.dots_filo.reserve(300000);
+ mesh.InitDots_filo(mask,0); //filopodium one by one
+ mesh.InitDots_filo(mask,1);
+ std::cout << "filo dots size=" << mesh.dots_filo.size() << "\n";
}
//renders the isotropic texture
--
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