ADD, minLength: removing all filopodium voxels from a mask if it

; (surface). This direction is orthogonal to filo axis.

; (surface). This direction is orthogonal to filo axis.

filoContourOrientedDensity	12

filoContourOrientedDensity	12

; Filopodium parameter:

; minimal length in microns of any filopodium (main filopodium or any branch)

; so that it is considered detectable and hence displayed in the

; ground truth final mask image -- shorter filopodia are not displayed

filoMinLength  0.6

; coarseness of initial Perlin noise in cell body (lower limit)

; coarseness of initial Perlin noise in cell body (lower limit)

coarsenessLower 1.0

coarsenessLower 1.0

; (surface). This direction is orthogonal to filo axis.

; (surface). This direction is orthogonal to filo axis.

filoContourOrientedDensity	4

filoContourOrientedDensity	4

; Filopodium parameter:

; minimal length in microns of any filopodium (main filopodium or any branch)

; so that it is considered detectable and hence displayed in the

; ground truth final mask image -- shorter filopodia are not displayed

filoMinLength  0.6

; coarseness of initial Perlin noise in cell body (lower limit)

; coarseness of initial Perlin noise in cell body (lower limit)

coarsenessLower 1.0

coarsenessLower 1.0

	//first, obtain a fresh volumetric mesh of the cell body

	//first, obtain a fresh volumetric mesh of the cell body

	sprintf(fn,"%s/ID%d/ID%d_t%03d_nucleus.vtk",path,ID,ID,fileNo);

	sprintf(fn,"%s/ID%d/ID%d_t%03d_nucleus.vtk",path,ID,ID,fileNo);

	std::cout << "reading cell body: " << fn << "\n";

	std::cout << "___reading cell body: " << fn << "\n";

	//keep the volumetric configuration of the first load

	//keep the volumetric configuration of the first load

	bool saveAlsoTetrahedra=(mesh.GetVolIDsize() == 0);

	bool saveAlsoTetrahedra=(mesh.GetVolIDsize() == 0);

				}

				}

				tipOffsets[idx].at((unsigned)fileNo)=(signed)iterTips->second;

				tipOffsets[idx].at((unsigned)fileNo)=(signed)iterTips->second;

				//debug report of calculated filopodia lengths

				const float l = mesh.calcFiloLength(iterTips->second);

				const int p = mesh.Ftree[iterTips->second].parent;

				std::cout << "filopodium ID " << idx << " (loaded as ID " << iterTips->second

				          << "): overall length: " << l << ", branches from: "

							 << (p>-1? p : 9999) << "\n";

				++iterTips;

				++iterTips;

			}

			}

		}

		}

	return(true);

	return(true);

}

}

//TODO:

//pokud neni videt TIP nebo delka je mensi nez parametr, tak smazat vsechny pixely od tohot filopodia a do textaku -1

#define DO_PHASE_II_AND_III

#define DO_PHASE_II_AND_III

#define DO_ANISOTROPIC_OUTPUT

#define DO_ANISOTROPIC_OUTPUT

int RenderMesh(const char* path,const int ID,int fileNo)

int RenderMesh(const char* path,const int ID,int fileNo)

	}

	}

 #endif

 #endif

#endif

#endif

	//save the mask image

	mask.SaveImage(fileName);

	//record voxel offsets within a mask image of all filopodia tips

	//record voxel offsets within a mask image of all filopodia tips

	const float xRes=mask.GetResolution().GetX();

	const float xRes=mask.GetResolution().GetX();

			const unsigned int i=(unsigned)tipIter->second.at((unsigned)fileNo);

			const unsigned int i=(unsigned)tipIter->second.at((unsigned)fileNo);

			const Vector3FC& realPos=mesh.Ftree[i].fPoints[mesh.Ftree[i].segToPoint.back()];

			const Vector3FC& realPos=mesh.Ftree[i].fPoints[mesh.Ftree[i].segToPoint.back()];

			//get pixel coordinate

			//get pixel coordinate

			const size_t x=size_t((realPos.x-xOff) *xRes);

			const unsigned int x=(unsigned)int((realPos.x-xOff) *xRes);

			const size_t y=size_t((realPos.y-yOff) *yRes);

			const unsigned int y=(unsigned)int((realPos.y-yOff) *yRes);

			const size_t z=size_t((realPos.z-zOff) *zRes);

			const unsigned int z=(unsigned)int((realPos.z-zOff) *zRes);

			//  inside mask image?                          &&   is displayed color == the expected one?

			if (mask.Include((signed)x,(signed)y,(signed)z) && mask.GetVoxel(x,y,z) == tipIter->first)

			{

				//tip is visible, save its pixel offset

				tipIter->second.at((unsigned)fileNo)=(int)mask.GetIndex(x,y,z);

				tipIter->second.at((unsigned)fileNo)=(int)mask.GetIndex(x,y,z);

				//save also the micron coordinate at the corresponding place

				//save also the micron coordinate at the corresponding place

				//into the coordinate structure

				//into the coordinate structure

				tipCoords[tipIter->first].at((unsigned)fileNo)=realPos;

				tipCoords[tipIter->first].at((unsigned)fileNo)=realPos;

			}

			}

			else

			{

				//tip is not visible

				int removedCnt=0;

				//remove all voxels of this color (tipIter->first)

				i3d::GRAY16* p = mask.GetFirstVoxelAddr();

				i3d::GRAY16* const pL = p + mask.GetImageSize();

				while (p != pL)

				{

					if (*p == tipIter->first) { *p=0; ++removedCnt; }

					++p;

				}

				std::cout << "WARN: REMOVING " << removedCnt << " PIXELS of filopodium ID " << tipIter->first << "\n";

				// declare the filopodium is not present in this time point

				tipIter->second.at((unsigned)fileNo)=-1;

				//tipCoords is -1 by initialization

			}

		}

		++tipIter;

		++tipIter;

	}

	}

	const size_t z=size_t((centreCoords[(unsigned)fileNo].z-zOff) *zRes);

	const size_t z=size_t((centreCoords[(unsigned)fileNo].z-zOff) *zRes);

	centreOffsets[(unsigned)fileNo]=(int)mask.GetIndex(x,y,z);

	centreOffsets[(unsigned)fileNo]=(int)mask.GetIndex(x,y,z);

	//save the mask image, finally (might have some pixels removed)

	mask.SaveImage(fileName);

	return(0);

	return(0);

}

}

- TM nacita spatne geometrie filo-offspringu

- TM nacita spatne geometrie filo-offspringu

- zajistit konzistenci mezi textaky a maskou - viz zdrojaky, main_Generator, l. 356

+ zajistit konzistenci mezi textaky a maskou - viz zdrojaky, main_Generator, l. 356

  - zobrazovat filopodium jedine pokud: je videt tip AND delka filopodia vetsi nez parameter

  + zobrazovat filopodium jedine pokud: je videt tip AND delka filopodia vetsi nez parameter

+ textak podobny tip_realCOords (udaje v micrometrech, na 4. desetinna mista), stejna struktura, vypisuje aktualni delku filopodia (nebo -1 pokud neexistuje)

+ textak podobny tip_realCOords (udaje v micrometrech, na 4. desetinna mista), stejna struktura, vypisuje aktualni delku filopodia (nebo -1 pokud neexistuje)

  (Martin uz udelal, waiting for merge)

  (Martin uz udelal, waiting for merge)