Overhaul radial distance utility

[connoramoreno]

Overhauls the radial distance utility. Changes include:

• Leveraging recent updates to the magnet workflow
• Code restructuring
• General code improvements
• Addition of a function to handle all radial distance utility functionality, removing the need to call several functions when using the utility
• Addition of a function to enforce helical symmetry in a matrix whose rows and columns correspond to regularly spaced angular arrays
• Addition of a function to smooth a matrix using Gaussian filtering without increasing the value of matrix elements

[connoramoreno]

I'm beginning to wonder if it might be worth converting this script to an object-oriented version

[gonuke]

I'm really impressed by the application of best practices here @connoramoreno - nice cleanup! I have a few more comments to continue the journey...

[gonuke]

Doesn't this assume even more than regular spacing? Doesn't it also assume:

1. that the matrix represents a full period, and
2. that there is a rib occurring at the mid-period
3. that the first rib is at the beginning of a period, ie. a place where poloidal symmetry is expected

[connoramoreno]

Good points. I thought I had written it in a way that (2) wouldn't matter but it seems that's not quite true. I think it's reasonable to assume (1) and (3), but I'd like to modify it to accommodate cases when (2) is not true.

[gonuke]

Can we update this docstring to clarify the additional assumptions?

[gonuke]

A little final polish...

[gonuke]

Just learned about chainging comparisons!

Suggested change

	if (min_tor_ang >= lower_bound or min_tor_ang <= upper_bound) or (
	max_tor_ang >= lower_bound or max_tor_ang <= upper_bound
	):
	in_toroidal_extent = True
	else:
	in_toroidal_extent = False
	in_toroidal_extent = ( (lower_bound <= min_tor_ang <= upper_bound) or
	(lower_bound <= max_tor_ang <= upper_bound) )

[gonuke]

Can we update this docstring to clarify the additional assumptions?

[gonuke]

Suggested change

	num_rows = matrix.shape[0]
	num_columns = matrix.shape[1]
	num_rows, num_columns = matrix.shape

[gonuke]

Suggested change

	for idx in range(num_rows):
	matrix[idx, -1] = matrix[idx, 0]
	matrix[:,-1] = matrix[:,0]

[gonuke]

Is this what it's doing?

Suggested change

	for idx, value in enumerate(
	flattened_matrix[: int(len(flattened_matrix) / 2)], start=1
	):
	flattened_matrix[-idx] = value
	half_period = flattened_matrix[0:int(len(flattened_matrix) / 2)]
	flattened_matrix = np.concatenate([half_period, np.flip(half_period)])

[gonuke]

Suggested change

	previous_iteration = matrix
	previous_matrix = matrix

[gonuke]

Suggested change

	previous_iteration,
	previous_matrix,

[gonuke]

Suggested change

	previous_iteration = smoothed_matrix
	previous_matrix = smoothed_matrix