CylBase Class Reference
#include <CylBase.h>
Public Member Functions | |
| CylBase (double x, double y, double z, double dia, double length, unsigned int numDivs) | |
| CylBase () | |
| void | setX (double v) |
| double | getX () const |
| void | setY (double v) |
| double | getY () const |
| void | setZ (double v) |
| double | getZ () const |
| void | setDia (double v) |
| double | getDia () const |
| void | setLength (double v) |
| double | getLength () const |
| void | setNumDivs (unsigned int v) |
| unsigned int | getNumDivs () const |
| void | setIsCylinder (bool v) |
| bool | getIsCylinder () const |
| double | volume (const CylBase &parent) const |
| Returns vol of current node. Usually needs to refer to parent. | |
| double | voxelVolume (const CylBase &parent, unsigned int fid) const |
| vector< double > | getCoordinates (const CylBase &parent, unsigned int entry) const |
| double | getDiffusionArea (const CylBase &parent, unsigned int index) const |
| double | getMiddleArea (const CylBase &parent, unsigned int index) const |
| Return cross-section area of middle of specified voxel. | |
| double | getVoxelLength () const |
| Return length of voxel. All are equal. | |
| double | selectGridSize (double h, double dia1, double granularity) const |
| void | matchCubeMeshEntries (const ChemCompt *other, const CylBase &parent, unsigned int startIndex, double granularity, vector< VoxelJunction > &ret, bool useCylinderCurve, bool useCylinderCap) const |
| double | nearest (double x, double y, double z, const CylBase &parent, double &linePos, double &r) const |
| double | nearest (double x, double y, double z, const CylBase &parent, unsigned int &index) const |
Detailed Description
Base class for cylinder calculations.
Constructor & Destructor Documentation
| CylBase::CylBase | ( | double | x, | |
| double | y, | |||
| double | z, | |||
| double | dia, | |||
| double | length, | |||
| unsigned int | numDivs | |||
| ) |
| CylBase::CylBase | ( | ) |
Member Function Documentation
| vector< double > CylBase::getCoordinates | ( | const CylBase & | parent, | |
| unsigned int | fid | |||
| ) | const |
Returns a vector with the coordinates of the specified MeshEntry. The MeshEntry (entry argument) is a voxel within this CylBase, 'entry' is indexed from 0 to numDivs. The parent is the parent CylBase with its own set of coords. The function does interpolation from the ends of the Node. These are detailed coordinates representative of the shape of the MeshEntry. For cylinders it is x1y1z1 x2y2z2 r0 r1 phi0 phi1 For spheres it is xyzdia.
Virtual function to return coords of mesh Entry. For Cylindrical mesh, coords are x1y1z1 x2y2z2 r0 r1 phi0 phi1
Referenced by NeuroMesh::vGetVoxelMidpoint().
| double CylBase::getDia | ( | ) | const |
Referenced by SpineEntry::psdCoords(), SpineEntry::rootArea(), SpineEntry::setVolume(), and NeuroMesh::vSetVolumeNotRates().
| double CylBase::getDiffusionArea | ( | const CylBase & | parent, | |
| unsigned int | fid | |||
| ) | const |
Returns diffusion cross-section from specified index to next. For index 0, this is cross-section to parent. For index numDivs-1, it is the cross-section from the second-last to the last voxel in this CylBase. Thus there is no valid value for (index == numDivs - 1), it has to be computed external to the CylBase, typically by calling the getDiffusionArea for the child CylBase.
Returns diffusion cross-section from specified index to previous. For index 0, this is cross-section area of parent. For index numDivs-1, it is the cross-section from the second-last to the last voxel in this CylBase. For index numDivs it is the area of this CylBase. Thus there is no valid value for (index > numDivs), it has to be computed external to the CylBase, typically by calling the getDiffusionArea for the child CylBase.
References PI.
Referenced by NeuroMesh::getAdx().
| bool CylBase::getIsCylinder | ( | ) | const |
| double CylBase::getLength | ( | ) | const |
| double CylBase::getMiddleArea | ( | const CylBase & | parent, | |
| unsigned int | index | |||
| ) | const |
Return cross-section area of middle of specified voxel.
Return the cross section area of the middle of the specified voxel.
References PI.
Referenced by NeuroMesh::updateCoords().
| unsigned int CylBase::getNumDivs | ( | ) | const |
| double CylBase::getVoxelLength | ( | ) | const |
Return length of voxel. All are equal.
Referenced by NeuroMesh::updateCoords().
| double CylBase::getX | ( | ) | const |
| double CylBase::getY | ( | ) | const |
| double CylBase::getZ | ( | ) | const |
| void CylBase::matchCubeMeshEntries | ( | const ChemCompt * | other, | |
| const CylBase & | parent, | |||
| unsigned int | startIndex, | |||
| double | granularity, | |||
| vector< VoxelJunction > & | ret, | |||
| bool | useCylinderCurve, | |||
| bool | useCylinderCap | |||
| ) | const |
| double CylBase::nearest | ( | double | x, | |
| double | y, | |||
| double | z, | |||
| const CylBase & | parent, | |||
| unsigned int & | index | |||
| ) | const |
| double CylBase::nearest | ( | double | x, | |
| double | y, | |||
| double | z, | |||
| const CylBase & | parent, | |||
| double & | linePos, | |||
| double & | r | |||
| ) | const |
References a, c, Vec::distance(), and Vec::pointOnLine().
Referenced by NeuroMesh::nearest(), nearest(), and NeuroMesh::updateShaftParents().
| double CylBase::selectGridSize | ( | double | h, | |
| double | dia1, | |||
| double | granularity | |||
| ) | const |
Utility commands for building interface to cube mesh
| void CylBase::setDia | ( | double | v | ) |
Referenced by NeuroNode::NeuroNode(), SpineEntry::setVolume(), SpineEntry::SpineEntry(), and NeuroMesh::vSetVolumeNotRates().
| void CylBase::setIsCylinder | ( | bool | v | ) |
Referenced by NeuroMesh::insertSingleDummy(), and SpineEntry::SpineEntry().
| void CylBase::setLength | ( | double | v | ) |
| void CylBase::setNumDivs | ( | unsigned int | v | ) |
Referenced by NeuroMesh::insertSingleDummy(), and SpineEntry::SpineEntry().
| void CylBase::setX | ( | double | v | ) |
| void CylBase::setY | ( | double | v | ) |
| void CylBase::setZ | ( | double | v | ) |
| double CylBase::volume | ( | const CylBase & | parent | ) | const |
Returns vol of current node. Usually needs to refer to parent.
The entire volume for a truncated cone is given by: V = 1/3 pi.length.(r0^2 + r0.r1 + r1^2) where the length is the length of the cone r0 is radius at base r1 is radius at top. Note that this converges to volume of a cone if r0 or r1 is zero, and to the volume of a cylinder if r0 == r1.
References PI.
Referenced by SpineEntry::setVolume(), SpineEntry::volume(), and NeuroMesh::vSetVolumeNotRates().
| double CylBase::voxelVolume | ( | const CylBase & | parent, | |
| unsigned int | fid | |||
| ) | const |
Returns volume of specified voxel (MeshEntry)
Returns volume of MeshEntry. This isn't the best subdivision of the cylinder from the viewpoint of keeping the length constants all the same for different volumes. Ideally the thinner segments should have a smaller length. But this is simple and so is the diffusion calculation, so leave it. Easy to fine-tune later by modifying how one computes frac0 and frac1.
References PI.
Referenced by NeuroMesh::updateCoords().
The documentation for this class was generated from the following files:
- mesh/CylBase.h
- mesh/CylBase.cpp
