# seen |= correctR
if len(resultR) > 0:
nonZeroCount += 1
extraCount += len(resultR - correctR)
missingCount += len(correctR - resultR)
# # print("{}/{} - {}".format(i, len(queryIsolates), isolate))
# print("{}/{} - {} - {}:{}".format(i+1, len(queryIsolates), isolate, len(resultR), len(correctR)))
# # print("\t{} --- {} / {} : {} / {}".format(isolate, len(resultR - correctR), len(resultR), len(correctR - resultR), len(correctR)))
if resultR == correctR:
correctCount += 1
if len(resultR) > 0:
nonZeroCorrectCount += 1
else:
print("\t{} ----- {}".format([(extraIsolate, [isolate.regionDist(extraIsolate, region) for region in cfg.regions]) for extraIsolate in resultR - correctR], [(missingIsolate, [isolate.regionDist(missingIsolate, region) for region in cfg.regions]) for missingIsolate in correctR -resultR]))
print("total correct: {}/{}".format(correctCount, queryCount))
print("nonEmpty correct: {}/{}".format(nonZeroCorrectCount, nonZeroCount))
print("total extra: {}, total missing: {}".format(extraCount, missingCount))
if __name__ == '__main__':
cfg = config.loadConfig()
isolates = pyroprinting.loadIsolates(cfg)
index = SpatialIndex(isolates, cfg)
correctNeighbors = fullsearch.getNeighborsMap(isolates, cfg)
# testSpatial(isolates, index, correctNeighbors, cfg)
cProfile.run("testSpatial(isolates, index, correctNeighbors, cfg)")
def computeDBscanClusters(isolates, cfg):
print("clustering for a subset of size {}...".format(cfg.isolateSubsetSize))
correctNeighbors = fullsearch.getNeighborsMap(isolates, cfg)
precomputedSearcher = fullsearch.PrecomputedIndex(correctNeighbors)
return dbscan(precomputedSearcher, cfg.radii, cfg.minNeighbors)
