AbstractCryptStatistics Class Reference
#include <AbstractCryptStatistics.hpp>
Public Member Functions | |
| AbstractCryptStatistics (MeshBasedCellPopulation< 2 > &rCrypt) | |
| virtual | ~AbstractCryptStatistics () |
| void | LabelSPhaseCells () |
| void | LabelAllCellsAsHealthy () |
| std::vector< bool > | AreCryptSectionCellsLabelled (std::vector< CellPtr > &rCryptSection) |
Protected Attributes | |
| MeshBasedCellPopulation< 2 > & | mrCrypt |
Detailed Description
Abstract crypt statistics class.Definition at line 40 of file AbstractCryptStatistics.hpp.
Constructor & Destructor Documentation
| AbstractCryptStatistics::AbstractCryptStatistics | ( | MeshBasedCellPopulation< 2 > & | rCrypt | ) |
Constructor.
- Parameters:
-
rCrypt The crypt
Definition at line 31 of file AbstractCryptStatistics.cpp.
| AbstractCryptStatistics::~AbstractCryptStatistics | ( | ) | [virtual] |
Destructor.
Definition at line 36 of file AbstractCryptStatistics.cpp.
Member Function Documentation
| void AbstractCryptStatistics::LabelSPhaseCells | ( | ) |
To recreate the virtual labelling experiments performed by Meineke et al (2001) in their off-lattice model of the intestinal crypt (doi:10.1046/j.0960-7722.2001.00216.x).
Cells which are in S phase are labelled using the CellLabel cell property.
In Owen Sansom's experiments this is called twice; once at the beginning and once at the end of an hour to simulate uptake of the label over an hour, so some cells will already be labelled when this is called the second time.
(assumption that S phase lasts longer than one hour is pretty sound)
Definition at line 40 of file AbstractCryptStatistics.cpp.
References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), CellPropertyRegistry::Instance(), and mrCrypt.
| void AbstractCryptStatistics::LabelAllCellsAsHealthy | ( | ) |
Set all the cells in the crypt to have the mutation state WildTypeCellMutationState.
Definition at line 60 of file AbstractCryptStatistics.cpp.
References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), CellPropertyRegistry::Instance(), and mrCrypt.
| std::vector< bool > AbstractCryptStatistics::AreCryptSectionCellsLabelled | ( | std::vector< CellPtr > & | rCryptSection | ) |
Get all cells within a cell width of the section defined as the line between points (xBottom,0) and (xTop,yTop). If a patricular cell is labelled then the boolean true is returned.
Periodicity can be taken into account (if xTop and xBottom are more than half a crypt width apart then a more realistic section will be across the periodic boundary), using the final parameter. This obviously requires the mesh to be cylindrical.
- Parameters:
-
rCryptSection vector of cells in the section (from a call to GetCryptSection in the concrete class)
- Returns:
- a standard vector of booleans which states whether a labelled cell is present at a corresponding position.
Definition at line 71 of file AbstractCryptStatistics.cpp.
Member Data Documentation
MeshBasedCellPopulation<2>& AbstractCryptStatistics::mrCrypt [protected] |
The crypt.
Definition at line 45 of file AbstractCryptStatistics.hpp.
Referenced by CryptStatistics::CellIsInSection(), CryptStatistics::CellIsInSectionPeriodic(), CryptStatistics::GetCryptSection(), CryptProjectionStatistics::GetCryptSection(), LabelAllCellsAsHealthy(), and LabelSPhaseCells().
The documentation for this class was generated from the following files:
- crypt/src/statistics/AbstractCryptStatistics.hpp
- crypt/src/statistics/AbstractCryptStatistics.cpp
