def cacheIsolateSubset(cfg):
cacheFileName = pyroprinting.getIsolatesCacheFileName(cfg)
if os.path.isfile(cacheFileName):
return
isolates = pyroprinting.loadIsolatesFromFile("isolatesAll.pickle")
isolateSubset = pyroprinting.getRandomSubset(isolates, cfg)
with open(cacheFileName, mode='w+b') as cacheFile:
pickle.dump(isolateSubset, cacheFile)
def loadIsolateList(filename):
cfg = config.loadConfig()
isolates = pyroprinting.loadIsolatesFromFile("isolatesAll.pickle")
isolateIdMap = {iso.name.strip(): iso for iso in isolates}
with open(filename) as listFile:
isoIds = {isoId.strip().strip("'").strip() for isoId in listFile.readline().split(',')}
# print(isoIds)
missingIsos = [iso.name for iso in isolates if iso.name.strip() not in isoIds]
extraIsos = [isoId for isoId in isoIds if isoId not in isolateIdMap]
print(extraIsos)
print("extraIsoCount: {}".format(len(extraIsos)))
print(missingIsos)
print("missingIsoCount: {}".format(len(missingIsos)))
sharedIsos = [iso for iso in isolates if iso.name.strip() in isoIds]
print("{}/{} shared".format(len(sharedIsos), len(isolates)))
with open("isolatesShared.pickle", mode='w+b') as cacheFile:
pickle.dump(sharedIsos, cacheFile)
# fullGetClusters = {frozenset(cluster) for cluster in fullGetClusters}
# fullPopClusters = {frozenset(cluster) for cluster in fullPopClusters}
preFullClusters = {frozenset(cluster) for cluster in preFullClusters}
# printClusters(preFullClusters)
# assert len(getMultipleClusterPoints(isolates, preFullClusters)) == 0
assert spatialPopClusters == preFullClusters
# assert spatialGetClusters == spatialPopClusters
# assert fullGetClusters == fullPopClusters
# assert verifyClusters(isolates, correctNeighbors, cfg.minNeighbors, clusters)
if __name__ == "__main__":
cfg = config.loadConfig()
# isolates = pyroprinting.loadIsolates(cfg)
isolates = pyroprinting.loadIsolatesFromFile("isolates{}.pickle".format(sys.argv[1]))
# correctNeighbors = fullsearch.getNeighborsMap(isolates, cfg)
print(sys.argv)
if sys.argv[2] == "spatial":
index = spatial.SpatialIndex(isolates, cfg)
elif sys.argv[2] == "fullsearch":
index = fullsearch.FullSearchIndex(isolates)
else:
print("bad index. use 'spatial' or 'fullsearch'")
if sys.argv[3] == "dbscan":
dbscan(index, cfg.radii, cfg.minNeighbors)
elif sys.argv[3] == "popDBSCAN":
popDBSCAN(index, cfg.radii, cfg.minNeighbors)
else:
