SimShow
SimShowAt
SimShowFinal
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Description

Return graphics images visulizing the results of a simulation, at a specific time, with the concentration of one particular species illustrated as a function of position. The concentration is represented by a range of colors, one color per cell.

Needs["Cellzilla2D`"];

Return Value

SimShow[solution, variable, time, template, {ColorMin, ColorMax}, {ValMin, ValMax}, options] returns a visualizaton at the specified time.

SimShow[solution, variable, time, template, {ColorMin, ColorMax}, {ValMin, ValMax}, options] returns a visualizaton at the specified time.

SimShowAt[solution, variable, time, template, {ColorMin, ColorMax}, threshold, options] - instead of interpolating between the two colors, choose the colors based on whether variable is greater or less than the threshold value.

SimShowAt[solution, variable, time, template, {ColorMin, ColorMax}, options] - plots a legend and autoscales the range.

SimShowFinal[solution, variable, template, {ColorMin, ColorMax}, options] - returns a visualization at the end time of the simulation. The legend is plotted and the range is autoscalled.

SimShowFinal[solution, variable, template, {ColorMin, ColorMax}, threshold, options] - returns a visualization at the end time of the simulation. Uses thresholding instead of interpolation. No legend.

solution - is the output of RunSim

variable - is any variable in the solution, e.g., if X is used, then the output will use the color of X[1][t] for cell 1, X[2][t] for cell 2, ...

template - is the template used to generate the reaction newtork with CelleratorNetwork.

{ColorMin, ColorMax} - Any two RGB colors; the color of of cell i is calculated from the value of X[i][t] using linear interpolation between ValMin and ValMax. Values less than the minimum or more than the maximum or plotted at ColorMin or ColorMax. These colors can either be color names such as Pink or RGB color specifications using RGBColor. A list of named colors can be found here.

SimShow[options]

SimShow[variable, options]

These two versions will prompt the user to select a solution file, which must have a filename SolutionXXXX.nb (e.g., the output of grow); and will look for a file with the name DTissueXXXX.nb for the tissue.

Options

In either mode, any option for ShowTissue may be used.

"variable"->variableName (in the first form.)

"Time"->time - if not specified, will auto-select the end of the solution interval.

"Colors"->{ColorMin, Colormax} - two color names should be given; if omitted, default values will be used.

"Values"->{min, max} - values of the variable that correspond to the colors rgbmin and rgbmax. If not specified, the max and min values of the variable in the solution wil lbe used.

"Legend"->True - True/False to display/suppress a legend.

"Tissue"->filename will override the default file name.

"Solution"->filename will override the file selection menu.

Example

[ Download Example as Zipped Mathematica Notebook ]

Implementation Notes

See Also

SimAnimate



[2012 Nov 11]