parser.add_argument('-t', '--type', dest='protocol_type', help='type of the protocol (for generating the ground truth): \
dhcp, dnp3, icmp, modbus, ntp, smb, smb2, tftp, zeroaccess')
parser.add_argument('-o', '--output_dir', dest='output_dir', default='tmp_netplier/', help='output directory')
parser.add_argument('-l', '--layer', dest='layer', default=5, type=int, help='the layer of the protocol')
parser.add_argument('-m', '--mafft', dest='mafft_mode', default='ginsi', help='the mode of mafft: [ginsi, linsi, einsi]')
parser.add_argument('-mt', '--multithread', dest='multithread', default=False, action='store_true', help='run mafft with multi threads')
args = parser.parse_args()
p = Processing(filepath=args.filepath_input, protocol_type=args.protocol_type, layer=args.layer)
# p.print_dataset_info()
mode = args.mafft_mode
if args.protocol_type in['dnp3']: # tftp
mode = 'linsi'
netplier = NetPlier(messages=p.messages, direction_list=p.direction_list, output_dir=args.output_dir, mode=mode, multithread=args.multithread)
fid_inferred = netplier.execute()
# Clustering
messages_aligned = Alignment.get_messages_aligned(netplier.messages, os.path.join(netplier.output_dir, Alignment.FILENAME_OUTPUT_ONELINE))
messages_request, messages_response = Processing.divide_msgs_by_directionlist(netplier.messages, netplier.direction_list)
messages_request_aligned, messages_response_aligned = Processing.divide_msgs_by_directionlist(messages_aligned, netplier.direction_list)
clustering = Clustering(fields=netplier.fields, protocol_type=args.protocol_type)
clustering_result_request_true = clustering.cluster_by_kw_true(messages_request)
clustering_result_response_true = clustering.cluster_by_kw_true(messages_response)
clustering_result_request_netplier = clustering.cluster_by_kw_inferred(fid_inferred, messages_request_aligned)
clustering_result_response_netplier = clustering.cluster_by_kw_inferred(fid_inferred, messages_response_aligned)
clustering.evaluation([clustering_result_request_true, clustering_result_response_true], [clustering_result_request_netplier, clustering_result_response_netplier])
