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Version 1.2 (June 2013)
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Version 1.2 (June 2013)
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Grid that will hold the epithelial cells on the bottom of a boundary (if specified) More...
Public Member Functions | |
| EpithelialGrid (Simulator aSim, XMLParser xmlRoot) | |
 Public Member Functions inherited from simulator.SpatialGrid | |
| SpatialGrid () | |
| Blank constructor. More... | |
| SpatialGrid (int nI, int nJ, int nK, double resolution) | |
| Default constructor for an empty spatial grid. More... | |
| SpatialGrid (int nI, int nJ, double resolution) | |
| Default constructor for an empty 2D spatial grid. More... | |
| boolean | isValid (DiscreteVector dC) |
| Determine if a given discrete position is valid or outside the grid (Padding excluded) More... | |
| boolean | isValidOrPadded (DiscreteVector dC) |
| Determine if a given discrete position is valid or outside the grid (Padding included) More... | |
| boolean | isValidorPadded (int i, int j, int k) |
| Determine if a given voxel coordinate is valid or outside the grid. More... | |
| boolean | isValid (ContinuousVector cc) |
| Determine if a given continuous location is valid or outside the grid. More... | |
| boolean | isValidOrPadded (ContinuousVector cc) |
| Test if a location is valid or is outside the grid. Note padding is included as valid. More... | |
| DiscreteVector | getDiscreteCoordinates (ContinuousVector cC) |
| Transform a location, expressed as a continuous vector into a discrete position on the basis of the resolution of the grid. More... | |
| ContinuousVector | getContinuousCoordinates (DiscreteVector dC) |
| Transform a position, expressed as a discrete vector into a continuous location on the basis of the resolution of the grid. More... | |
| ContinuousVector | getContinuousCoordinates (int i, int j, int k) |
| Convert a set of voxel coordinates into a continuous vector. More... | |
| double | getMax () |
| Return the maximum value on this grid (padding included) More... | |
| double | getAverage () |
| Return the average value on this grid (padding included) More... | |
| double | getSum () |
| Return the sum of this grid. More... | |
| double | getMin () |
| Return the minimum value on this grid (padding included) More... | |
| double | diff2X (int i, int j, int k) |
| For a given location, calculate the 2nd spatial derivative according to X. More... | |
| double | diff2X (DiscreteVector dV) |
| For a given location, expressed as a discrete vector, calculate the 2nd spatial derivative according to X. More... | |
| double | diffX (int i, int j, int k) |
| For a given location, calculate the 1st spatial derivative according to X. More... | |
| double | diffX (DiscreteVector dV) |
| For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to X. More... | |
| double | diff2Y (int i, int j, int k) |
| For a given location, calculate the 2nd spatial derivative according to Y. More... | |
| double | diff2Y (DiscreteVector dV) |
| For a given location, expressed as a discrete vector, calculate the 2nd spatial derivative according to Y. More... | |
| double | diffY (int i, int j, int k) |
| For a given location, calculate the 1st spatial derivative according to Y. More... | |
| double | diffY (DiscreteVector dV) |
| For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to Y. More... | |
| double | diff2Z (int i, int j, int k) |
| For a given location, calculate the 2nd spatial derivative according to Z. More... | |
| double | diffZ (int i, int j, int k) |
| For a given location, calculate the 1st spatial derivative according to Z. More... | |
| double | diffZ (DiscreteVector dV) |
| For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to Z. More... | |
| double | getValueAround (ContinuousVector cC, double extReso) |
| Computes the average concentration seen in a sphere (or cube) centered around a given point. More... | |
| double | getValueAround (LocatedAgent aLocAgent) |
| Returns the average grid value seen in a sphere (or cube) located around a given agent. More... | |
| double | getValueAt (ContinuousVector cC) |
| Return the value stored at the location given by the stated continuous vector. More... | |
| ContinuousVector | getGradient (ContinuousVector cC) |
| Returns a vector of the first spatial derivatives in x, y & z. More... | |
| ContinuousVector | getGradient2D (ContinuousVector cC) |
| Returns a vector of the first spatial derivatives in x and y, for 2D simulations. More... | |
| double | getValueAt (DiscreteVector dV) |
| Return the value on the padded grid at a given position (the coordinates are NOT corrected) More... | |
| double | getValueAt (int i, int j, int k) |
| Return the value on the padded grid at a given position (the coordinates are NOT corrected) More... | |
| void | setValueAt (double value, ContinuousVector cC) |
| Set a grid location, expressed as a ContinuousVector, to a specified value. The coordinates are corrected. More... | |
| void | setValueAt (double value, DiscreteVector dC) |
| Set a grid location, expressed as a DiscreteVector, to a specified value. The coordinates are corrected. More... | |
| void | setValueAt (double value, int i, int j, int k) |
| Set a grid location to a specified value. Note the coordinates are NOT corrected. More... | |
| void | addValueAt (double value, ContinuousVector cC) |
| Add a value to that contained at the given discrete coordinates of this grid. Coordinates are corrected for padding. More... | |
| void | addValueAt (double value, DiscreteVector dC) |
| Add a value to that contained at the given discrete coordinates of this grid. Coordinates are corrected for padding. More... | |
| void | addAllValues (double value) |
| Add a value to all locations on this grid (including the padding) More... | |
| void | truncateValueAt (int i, int j, int k) |
| Checks a value at a given location and sets it to zero if the value is negative. More... | |
| void | setAllValueAt (double value) |
| Set all meshes of a grid with the same value (including the padding - if not a chemostat run) More... | |
| int | getGridSizeI () |
| Return the number of voxels in the X direction. More... | |
| int | getGridSizeJ () |
| Return the number of voxels in the Y direction. More... | |
| int | getGridSizeK () |
| Return the number of voxels in the Z direction. More... | |
| int | getGridTotalSize (int axeCode) |
| Return the number of voxels along a given direction (axeCode) More... | |
| double | getGridLength (int axeCode) |
| Returns the length (in distance unit) along a given direction. More... | |
| double | getVoxelVolume () |
| Return the volume of one voxel of the spatial grid. More... | |
| double[][][] | getGrid () |
| Return the whole grid including the padding. More... | |
| double[][][] | getCloneGrid () |
| Return a clone of this spatial grid. More... | |
| double | getResolution () |
| Returns the resolution of this spatial grid. More... | |
| boolean | is3D () |
| Determine if this spatial grid is 3D or 2D. More... | |
| void | setGrid (double[][][] u) |
| Set the values of this spatial grid to those contained in the supplied grid. More... | |
| void | writeReport (ResultFile bufferState, ResultFile bufferSummary) throws Exception |
| Write the contents of this grid to the XML results files. More... | |
Additional Inherited Members | |
| Public Attributes inherited from simulator.SpatialGrid | |
| String | gridName |
| String | gridUnit = "g.L-1" |
| double[][][] | grid |
| Protected Member Functions inherited from simulator.SpatialGrid | |
| void | initGrids () |
| Creates the solute grid at the required size. More... | |
| Protected Attributes inherited from simulator.SpatialGrid | |
| int | _nI |
| int | _nJ |
| int | _nK |
| double | _reso |
| boolean | _is3D |
Grid that will hold the epithelial cells on the bottom of a boundary (if specified)
Class for creating a grid of epithelial cell agents on the bottom of a domain. This replaces the notion of the solid substratum that existed in previous versions of iDynoMiCS. Note that this grid of cells is still placed above the y0z boundary condition
1.8.3.1
