Global

Methods

CopyGridODEs(cols, rows, template)

Make a back-up of all the ODE states (for synchronous ODE updating)
Parameters:
Name Type Description
cols int Width of the grid
rows int Height of the grid
template 2DArray Get ODE states from here
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MakeGrid(cols, rows, template)

Make a grid, or when a template is given, a COPY of a grid.
Parameters:
Name Type Description
cols int Width of the new grid
rows int Height of the new grid
template 2DArray Template to be used for copying (if not set, a new empty grid is made)
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applyKernelFFT(gridmodel, readProp, writeProp, kernelObj, scaleopt)

Apply a 2-D FFT convolution to one numeric state of every gridpoint. Reads from readProp, writes to writeProp (may be the same property). Low-level engine used by diffuseStatesFFT and castDiskFFT. Works in both browser and Node.js.
Parameters:
Name Type Attributes Default Description
gridmodel object
readProp string
writeProp string
kernelObj Object
scale number <optional>
 1
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copy(aObject)

Deep copy function.
Parameters:
Name Type Description
aObject Object Object to be deep copied. This function still won't deep copy every possible object, so when enabling deep copying, make sure you put your debug-hat on!
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default_colours()

Compile a dict of default colours if nothing is given by the user. Reuses colours if more colours are needed.
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dict_reverse(obj)

Reverse dictionary
Parameters:
Name Type Description
obj Object dictionary-style object to reverse in order
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diffuseStateGPU(gridmodel, state, kernelObj)

Diffuse a continuous state using GPU (WebGL2) separable Gaussian convolution. Two fragment shader passes (H then V). Faster than FFT for large grids. Browser only — silently falls back to a console warning in Node. GPU context and shaders are lazily created and cached on the gridmodel.
Parameters:
Name Type Description
gridmodel object
state string
kernelObj object from makeGaussianKernel
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get2DFromCanvas(canvas) → {2DArray}

Reconstruct a 2D array based on a canvas
Parameters:
Name Type Description
canvas canvas HTML canvas element to convert to a 2D grid for Cacatoo
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Returns:
Returns a 2D array (i.e. a grid) with the states
Type
2DArray

hexToRGB(hex)

Convert hexadecimal to RGB
Parameters:
Name Type Description
hex String string to convert to RGB
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makeDiskKernel(radius) → {Object}

Build a flat disk (top-hat) kernel for use with castDiskFFT. Cells within radius get value 1, cells outside get 0. NOT normalised. This means castDiskFFT deposits exactly `amount` at EACH cell within the disk around each source — not `amount` spread across the disk area. That matches the typical biological interpretation: every cell within range receives the full benefit from a nearby source cell.
Parameters:
Name Type Description
radius number Disk radius in grid cells
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Returns:
Type
Object

makeGaussianKernel(sigma_x, sigma_yopt) → {Object}

Build a normalised Gaussian kernel for use with both diffuseStatesFFT and diffuseStateGPU. Returns one object with everything both methods need. Build it once, pass it to either method. Pass only sigma_x for isotropic (symmetric) diffusion. Pass both for anisotropic: sigma_x = horizontal spread (x/columns), sigma_y = vertical spread (y/rows).
Parameters:
Name Type Attributes Description
sigma_x number Horizontal spread in grid cells.
sigma_y number <optional>
 Vertical spread. Defaults to sigma_x.
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Returns:
Type
Object
Example
sim.model.k = makeGaussianKernel(3)        // symmetric
sim.model.k = makeGaussianKernel(8, 1)     // wide in x, narrow in y
this.diffuseStatesFFT('signal', null, this.k)  // FFT path
this.diffuseStateGPU('signal',  null, this.k)  // GPU path

nameToRGB(name)

Convert colour name to RGB
Parameters:
Name Type Description
name String string to look up in the set of known colours (see below)
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parseColours(cols)

Make sure all colours, even when of different types, are stored in the same format (RGB, as cacatoo uses internally)
Parameters:
Name Type Description
cols Array array of strings, or [R,G,B]-arrays. Only strings are converted, other returned.
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pause()

Below are a few global functions that are used by Simulation classes, but not a method of a Simulation instance per se
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random_colours()

A list of default colours if nothing is given by the user.
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shuffle(array, rng)

Randomly shuffle an array with custom RNG
Parameters:
Name Type Description
array Array array to be shuffled
rng MersenneTwister MersenneTwister RNG
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stringToRGB(string)

Convert colour string to RGB. Works for colour names ('red','blue' or other colours defined in cacatoo), but also for hexadecimal strings
Parameters:
Name Type Description
string String string to convert to RGB
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