Clean up fundus/pits extraction

[binarybottle]

General

• many of your functions don’t list and adequately explain all of your Parameters.
• name consistently and according to PEP8 naming conventions!
• replace all xrange with range (for forward compatibility with python3, and no need for the “0,” in range(0, blah)

  libbasin.py

def fcNbrLst(FaceDB, Hemi):

you can replace this with mesh.py’s new find_adjacent_faces()

def vrtxNbrLst(VrtxNo, FaceDB, Hemi):

you can replace this with mesh.py’s find_neighbors() or find_neighbors_vertex()

def compnent(FaceDB, Basin, NbrLst, PathHeader):

i don’t understand what this function does. rename Parameters consistently and according to PEP8 naming conventions:

• faces, basin_faces, neighbor_list, path_header
• (copy definitions from other functions)

rename function to something clearer:

• find_basin_neighbors()?
• find_basin_connected_faces()?

def judgeFace1(FaceID, FaceDB, CurvatureDB, Threshold = 0):

rename function to something clearer:

• test_face_curvature()?
• test_face_zero_order_curvature()?

rename Parameters consistently and according to PEP8 naming conventions:

• face_index, faces, curvatures, threshold

def basin(FaceDB, CurvatureDB, Threshold = 0): return Basin, Left

rename Parameters consistently and according to PEP8 naming conventions:

• faces, curvatures, threshold

rename Returns:

• basin_faces, nonbasin_faces

rename function to something clearer:

• extract_basin_faces()?

def allTrue(List):

superfluous function -- remove

def dfsSeed(Visited, Basin):

too little to warrant a function; remove and include line of code where the function is called

def dfs(Seed, Basin, Visited, NbrLst, FaceDB): return Visited, FcMbr, VrtxMbr

rename Parameters consistently and according to PEP8 naming conventions:

• seed_vertex, basin_vertices?, visited_vertices?, neighbor_list

rename Returns:

• visited_vertices?, face_member, vertex_member

rename function to something clearer:

• basin_depth_first_search()?

the following appends vertices, not faces, so what is going on?:
FcMbr = [] # members that are faces of this connected component

def pmtx(Adj):

superfluous function -- remove

def all_same(items):

too little to warrant a function; remove and include line of code where the function is called

def univariate_pits(CurvDB, VrtxNbrLst, VrtxCmpnt, Thld): return B, C, Child

rename Parameters consistently and according to PEP8 naming conventions:

• curvatures, vertex_neighbor_list, ?, threshold

rename Returns to something clearer (i don’t know what they mean), and rename function to something clearer:

• extract_univariate_pits()?

def clouchoux(MCurv, GCurv):

this function is called only within clouchoux_pits(), so remove this function and replace “if clouchoux(MCurv[i], GCurv[i]):” with: “if (MCurv > 0.2) and (GCurv < 0):” and include 0.2 as a Parameter.

def clouchoux_pits(Vertexes, MCurv, GCurv):

rename Parameters consistently and according to PEP8 naming conventions:

• vertices, mean_curvatures, gaussian_curvatures
• pits

rename function to something clearer:

• extract_clouchoux_pits()?

def getBasin_and_Pits(Maps, Mesh, SulciVTK, PitsVTK, SulciThld = 0, PitsThld = 0, Quick=False, Clouchoux=False, SulciMap='depth'):

remove extraneous Parameters and code, rename Parameters consistently and according to PEP8 naming conventions, and rename function to something clearer:

• extract_basins_pits()?

  libfundi.py

All of the general comments for libbasin.py above apply.

Re: Prim and mst -- how do these differ from the x/min_span_tree.py code?

Minimum spanning tree is general-purpose enough that it should be in utils/paths.py

Best to remove the random from downsample() -- we want everything to be replicable.

[binarybottle]

I will close this issue, as the line-based fundus extraction is not currently being used by Mindboggle.