Okay so this code is very precariously built due to unforseen issues requiring code to be added on but be reliant on old code that changes
So I'm gonna summarize the order of programs and dependencies for future me (hopefully not anyone else. If anyone else is reading this, I apologize.)


main.m runs these:
	(Zeroth - not because of computer indexing, but because I don't think this one really needs to be explained) inputPts.m
	Literally just reads in a text file of nx3 coordinates, and puts it into a nx3 array

	First, vectors.m
	This takes in an array of points, and fits a circle to it.
	Rotates the circle to be parallel to the xy plane - z is same for all
	Then, if finds a point every t degrees (set at the top) along that circle
	Since we're pretending this is at the origin for x y, the direction vector is literally just [x,y] normallized
	Find dirNum (global variable) points along each direction vector, this gets saved in lines
	Unrotate lines to get points
	main then writes these to a file - output.txt
	(in my defense of the name, I did not know I was going to be writing more than 1 output file at the time)

Second, results.m
This opens output.txt, and the stl file, and uses a bunch of functions I did not write to calculate the point of the closest distance on the surface made by the stl file.
spts stores all the points.
Then I find which face of the stl it belongs to by comparing the vector made by the surface point and a vertex of the face with the normal of the face (should be perpindicular = dot product 0)
	- never exatly 0, so just the minimum
We also have to check if the dot is within the triangle of the face due to multiple faces having the same normal
The distances, surface points and normals are all written to text files
We actually only care about 'distances.txt' and 'surface points.txt'

Third, circleFit
When we ran angles and then the VS program Snowman, we found that much of the area under the breast was not found due to the straight lines
So instead, we decided to try to fit a sphere to the surface points and then get points from that
This function uses surface points.txt to fit a sphere. It first pulls out the first thresh points of each line (again, relies on global dirNum)
	- many of the points towards the end of each line were part of the chest wall, and not spherical
Once again, it fits a circle to the points from the input file (same as vector) and rotates to be parallel to the xy plane
Finds points on circle every t degrees
Finds a point along the straight vector every space (distance)
Calculates the direction vector from the center of the sphere to that point
Places a point along that direction vector radius of sphere away = point on surface of sphere (along line on surface of sphere originating from fitted circle)
Assumes z is 0
Saves in lines
Rotates lines (something went a little screwy here, had to multiply by -1, don't know why)
Writes these points to output2.txt
*While this can be run along to produce output2, if dirNum changes, since circleFit is dependent on surface points, which are dependent on vectors, the entire thing must be re-run


3.5, results
Need to run results with output2.txt to get surface points and normals again

Fourth, angles.m
This reads normals.txt, and compares neighbours in each set of dirNum points
Writes to a file angles.txt
(I swear we're missing some angles. With t = 0, we should have 36 lines, with dirNum = 30, each line had 30 points and 29 angles = 1044 angles. But only 1043 lines are in file. It gets worse as dirNum increases?)

Summary, run.m
I kept losing track of what I needed to run and in what order, so I made run to just do it all for me.
Then I figured I might want to write a README file so that if I need to do some more adjustments later I could read this and get a relatively in depth description of what the hell I was doing.

In short: run main->results("output.txt")->results->circleFit->results("output2.txt")->angles
Then you can run the VS program Snowman.
Or just run run.m