From 833bdbac88a6ee3c8a7e048d3d9a8e26f8120b5a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vladim=C3=ADr=20Ulman?= <ulman@mpi-cbg.de>
Date: Thu, 13 Oct 2016 01:22:46 +0200
Subject: [PATCH] Added LoadNewMesh() and RenderMesh(), added loading of sample
sequence.
---
cmath3d/TriangleMesh.cpp | 2 +-
src/graphics.cpp | 4 +-
src/main.cpp | 105 ++++++++++++++++++++++++++++-----------
3 files changed, 80 insertions(+), 31 deletions(-)
diff --git a/cmath3d/TriangleMesh.cpp b/cmath3d/TriangleMesh.cpp
index 8e1eb64..658b26a 100644
--- a/cmath3d/TriangleMesh.cpp
+++ b/cmath3d/TriangleMesh.cpp
@@ -401,7 +401,7 @@ int ActiveMesh::ImportVTK_Volumetric(const char *filename)
int ActiveMesh::ImportVTK_Ftree(const char *filename,bool resetMesh)
{
const int PointsOnRadiusPeriphery=10;
- const float radiusCorrection=0.2f;
+ const float radiusCorrection=0.1f;
if (resetMesh)
{
diff --git a/src/graphics.cpp b/src/graphics.cpp
index 0af17c1..7234685 100644
--- a/src/graphics.cpp
+++ b/src/graphics.cpp
@@ -57,13 +57,15 @@ bool showVertexSurface=false;
bool showQuadricSurface=false;
bool showTEST=false;
+int LoadNewMesh(int fileNo);
+int RenderMesh(int fileNo);
///manage \e count steps of the simulation and then print and draw
void step(int count)
{
while ((params.currTime < params.stopTime) && (count > 0))
{
- //do some job
+ LoadNewMesh(int(params.currTime));
params.currTime += params.incrTime;
--count;
diff --git a/src/main.cpp b/src/main.cpp
index 5801cae..eba0f1c 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -10,37 +10,28 @@ void ParamsSetup(void);
//
ActiveMesh mesh;
+int LoadNewMesh(int fileNo);
+int RenderMesh(int fileNo);
int main(void)
{
ParamsSetup();
- //load mesh
+/*
+ //SURFACE FITTING:
+
//char filename[]="../sample_input/samplecell.stl";
//char filename[]="../sample_input/torus_100_30.stl";
char filename[]="../sample_input/sphere.stl";
- char VTKfile[]="../sample_input/ID1_t001_nucleusSurf2148.vtk"; //surface
- //char VTKfile[]="../sample_input/ID1_t001_nucleus2038.vtk"; //volumetric
-
- //int retval=mesh.ImportSTL(filename);
- int retval=mesh.ImportVTK(VTKfile);
- //int retval=mesh.ImportVTK_Volumetric(VTKfile);
+ int retval=mesh.ImportSTL(filename);
if (retval)
{
std::cout << "some error reading file: " << retval << "\n";
return(1);
}
- retval=mesh.ImportVTK_Ftree("../sample_input/ID1_t001_fTree01.vtk");
- retval=mesh.ImportVTK_Ftree("../sample_input/ID1_t001_fTree02.vtk");
- if (retval)
- {
- std::cout << "some error reading f-tree: " << retval << "\n";
- return(2);
- }
-
- //std::cout << "mesh: " << filename << "\n";
+ std::cout << "mesh: " << filename << "\n";
std::cout << "vertices #: " << mesh.Pos.size() << "\n";
std::cout << "triangles #: " << mesh.ID.size()/3 << "\n";
std::cout << "normals #: " << mesh.norm.size() << "\n";
@@ -48,22 +39,17 @@ int main(void)
mesh.CenterMesh(params.sceneCentre);
//work with mesh
-/*
float surf_coeff[10];
mesh.CalcQuadricSurface_Taubin(10,surf_coeff);
*/
+
+ //ISBI:
+ LoadNewMesh(0);
+
+
/*
//render mesh
- i3d::Image3d<i3d::GRAY16> mask;
- mask.SetOffset(i3d::Offset(0.0,0.0,0.0));
- //mask.SetResolution(i3d::Resolution(20.0,20.0,20.0)); //for torus
- //mask.MakeRoom(300,300,300);
- mask.SetResolution(i3d::Resolution(2.0,2.0,2.0)); //for sample cell
- mask.MakeRoom(600,600,600);
- mask.GetVoxelData()=0;
- mesh.RenderMask(mask);
- mask.SaveImage("mesh.ics");
*/
initializeGL();
@@ -99,9 +85,9 @@ void ParamsSetup(void)
//adapted for cell cycle length of 24 hours
params.cellCycleLength=14.5*60; //[min]
- params.currTime=0.f; //all three are in units of minutes
- params.incrTime=0.1f;
- params.stopTime=5000.f;
+ params.currTime=0.0f; //all three are in units of minutes
+ params.incrTime=1.0f;
+ params.stopTime=50.0f;
params.imgSizeX=500; //pixels
params.imgSizeY=500;
@@ -115,3 +101,64 @@ void ParamsSetup(void)
params.imgPhCFilename="PhCImg%05d.tif";
params.tracksFilename="tracks.txt";
}
+
+
+int LoadNewMesh(int fileNo)
+{
+ char VTK_nucleusSurf[1024];
+ char VTK_nucleus[1024];
+ char VTK_fTreeA[1024];
+ char VTK_fTreeB[1024];
+
+ sprintf(VTK_nucleusSurf,"../sample_sequence/ID05_t%03d_nucleusSurf.vtk",fileNo);
+ sprintf(VTK_nucleus, "../sample_sequence/ID05_t%03d_nucleus.vtk",fileNo);
+ sprintf(VTK_fTreeA, "../sample_sequence/ID05_t%03d_fTree01.vtk",fileNo);
+ sprintf(VTK_fTreeB, "../sample_sequence/ID05_t%03d_fTree02.vtk",fileNo);
+
+ int retval=mesh.ImportVTK(VTK_nucleusSurf);
+ //int retval=mesh.ImportVTK_Volumetric(VTK_nucleus);
+ if (retval)
+ {
+ std::cout << "some error reading nucleus: " << retval << "\n";
+ return(1);
+ }
+
+ retval=mesh.ImportVTK_Ftree(VTK_fTreeA);
+ if (retval)
+ {
+ std::cout << "some error reading f-tree: " << retval << "\n";
+ return(2);
+ }
+
+ retval=mesh.ImportVTK_Ftree(VTK_fTreeB);
+ if (retval)
+ {
+ std::cout << "some error reading f-tree: " << retval << "\n";
+ return(2);
+ }
+
+ mesh.CenterMesh(params.sceneCentre);
+ std::cout << "loaded mesh #" << fileNo << "\n";
+
+ return(0);
+}
+
+
+int RenderMesh(int fileNo)
+{
+ i3d::Image3d<i3d::GRAY16> mask;
+ mask.SetOffset(i3d::Offset(0.0,0.0,0.0));
+ //mask.SetResolution(i3d::Resolution(20.0,20.0,20.0)); //for torus
+ //mask.MakeRoom(300,300,300);
+ mask.SetResolution(i3d::Resolution(2.0,2.0,2.0)); //for sample cell
+ mask.MakeRoom(600,600,600);
+ mask.GetVoxelData()=0;
+ mesh.RenderMask(mask);
+
+ char fileName[1024];
+ sprintf(fileName,"mesh_t%03d.tif");
+ mask.SaveImage(fileName);
+ std::cout << "rendered mesh #" << fileNo << "\n";
+
+ return(0);
+}
--
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