Explanation.txt

Main

	Fetch the scene image based on the name supplied
	create a simulator as an instance of the WaveSimulator2D class with the dimensions of the scene image	
	Create a visualizer based on the WaveVisualizer based on two color maps and inversion and black level stings
	Load the scene data from the image using load_scene_from_image
		- set the wave simulation refractive index values based on the red data byte [0] from each image point
		- set a field average: in principle we want to retrieve this from the wave
		- set the wave simulation field value starting condition from the green data  byte [1] from each image point
		- set the wave simulation damping values based on the blue values 

	Create 2 video writers that can write images using the image scene dimensions. These can be used to write the movies, third parameter is frames per second
	run the simulation for a number of time steps using the num_iterations value
		A. simulator.up.update_field 
			Calculate the Laplacian of the current field
			1: create a new field matrix for the damping using the current field value (u) previous field value (u_prev) and the damping field value (d)
			2: create new field (r) using the current field (u), the Laplacian and the damping field (d) and the speed field
			3: make the previous field (u_prev) the current field (u)
			4: make the current field u
			5: increase the time value	
		B. simulator.compute_strain_and_new_IOR parameters are the refractive_persistence, scaling factor, non_lin_constant_value and the exponent
			1: create du_dx and du_dy derivative kernals and a wave speed field
			2: calculate the strain_field from the du_dx and du_dy values
			3: calculate the current index of refraction field using a previous value and the strain value
			4 set the speed field from the index of refraction field
		C. update the visualizer using the data contained in the simulator instance
			show any data on screen as show field

what goes wrong: the current range for the refractive index is very low 1-2,5. This means that speed differences can only of this order. what we could do use a different definition for the lowest refractive index, for example an integer value of 10 or 50 (this version uses 50). This would allow us to define higher initial refractive indices