Tubegen/bugs and feature requests

Slowdown

Streamtube generation gets slower and slower as the program runs. What's going on? Is it running out of memory, reading inefficiently through a big file, doing something probabilistic that gets less likely the more tubes there are? We need a speedup!

In streamtube.cpp, function tube_collection_generator::generateSpacing(), unless getCullingDistance() == 0.0 (set this by passing -cd 0.0 to tubegen), a pairwise inter-tube distance-based culling check happens after each streamtube is generated, for a total complexity of O(n²).

It would be a good idea to separate out seeding, streamline/tube generation, and culling, since each of these can be modified or optimized separately. There's a lot of code repetition in streamtube.cpp --- . Also want to figure out the function of tube_collection_generator::getDistThreshold() (-dth argument to tubegen) in streamtube::avgdistance().

Just in streamtube.cpp, there's:

• void brown_streamtube::generate(double seed_point[3])
• void MC_streamtube::generate(double seed_point[3])
• void cross_fiber::generate(double seed_point[3])
• void tube_collection_generator::generate2()
• void tube_collection_generator::generatecross()
• void tube_collection_generator::generatecrossradii()
• void tube_collection_generator::generatehalfcircle()
• streamtube* tube_collection_generator::generateOneTube(double p[3])
• void tube_collection_generator::generate(int MC)
• void tube_collection_generator::generateSpacing(double sspace[3], int MC)
• void jot_tube_mesh_generator::generate()

These obviously do different things but there seems to be a lot of repeated code among them that should be factored out. Some of them are truly enormous functions, too, and should be broken apart for clarity.