Fixed a serious bug in DynamicPersistenceTrails + LSVineyard sorts filtration by attachment + miscellanea:
* added program options to pdbdistance-vineyard
* pdbdistance-vineyard takes frame list in a file
* more logging
* verification of pairing after vertex transpositions (commented out)
def add_simplices(zz, simplices, complex, birth, report_local = False):
deaths = []
for s in simplices:
i,d = zz.add([complex[sb] for sb in s.boundary], (s.dimension(), birth))
complex[s] = i
if d is not None:
if report_local or not d == birth:
deaths.append(d)
return deaths
def remove_simplices(zz, simplices, complex, birth, report_local = False):
deaths = []
for s in simplices:
d = zz.remove(complex[s], (s.dimension(), birth))
complex[s] = None
if d is not None:
if report_local or not d == birth:
deaths.append(d)
return deaths