if __name__ == '__main__':
parser = optparse.OptionParser(usage='%prog [--mpi] [--print] script', version=pyproct.__version__)
parser.add_option('--mpi', action="store_true", dest = "use_mpi", help="Add this flag if you want to use MPI-based scheduling.")
parser.add_option('--print', action="store_true", dest = "print_messages", help="Add this flag to print observed messages to stdout.")
options, args = parser.parse_args()
if(len(args)==0):
parser.error("You need to specify the script to be executed.")
json_script = args[0]
parameters = None
try:
parameters = ProtocolParameters.get_params_from_json(tools.remove_comments(open(json_script).read()))
parameters["global"]["workspace"]["base"] = os.path.abspath(parameters["global"]["workspace"]["base"])
except ValueError, e:
print "Malformed json script."
print e.message
exit()
observer = None
cmd_thread = None
if options.use_mpi:
from pyproct.driver.mpidriver import MPIDriver
from pyproct.driver.observer.MPIObserver import MPIObserver
observer = MPIObserver()
if options.print_messages:
cmd_thread = CmdLinePrinter(observer)
cmd_thread.start()
# Saving matrices
for dataset_name in data.all_datasets:
handler = MatrixHandler(condensed_matrices[dataset_name],
{"method": "load"})
handler.save_matrix("./matrices/%s" % dataset_name)
# Run pyProCT for each of them
base_script = "".join(open("base_script.json", "r").readlines())
for dataset_name in ['concentric_circles'
]: #data.all_datasets: #["spaeth_06"]:#
print dataset_name
# Change placeholders
script_str = base_script % (os.path.abspath(
"./tmp/%s" % dataset_name), "./matrices/%s" % dataset_name)
parameters = ProtocolParameters.get_params_from_json(script_str)
# And change another hypothesis stuff
parameters["clustering"]["evaluation"]["maximum_noise"] = data.noise[
dataset_name]
parameters["clustering"]["evaluation"][
"minimum_cluster_size"] = data.minsize[dataset_name]
parameters["clustering"]["evaluation"][
"minimum_clusters"] = data.num_cluster_ranges[dataset_name][0]
parameters["clustering"]["evaluation"][
"maximum_clusters"] = data.num_cluster_ranges[dataset_name][1]
print parameters["clustering"]["evaluation"][
"minimum_clusters"], parameters["clustering"]["evaluation"][
"maximum_clusters"]
if dataset_name in data.criteria:
parameters["clustering"]["evaluation"][
"evaluation_criteria"] = data.criteria[dataset_name]
create_directory("./matrices")
create_directory("./tmp")
condensed_matrices, all_observations = vtools.create_matrices(data)
# Saving matrices
for dataset_name in data.all_datasets:
handler = MatrixHandler(condensed_matrices[dataset_name], {"method":"load"})
handler.save_matrix("./matrices/%s"%dataset_name)
# Run pyProCT for each of them
base_script = "".join(open("base_script.json","r").readlines())
for dataset_name in ['concentric_circles']: #data.all_datasets: #["spaeth_06"]:#
print dataset_name
# Change placeholders
script_str = base_script%(os.path.abspath("./tmp/%s"%dataset_name),"./matrices/%s"%dataset_name)
parameters = ProtocolParameters.get_params_from_json(script_str)
# And change another hypothesis stuff
parameters["clustering"]["evaluation"]["maximum_noise"] = data.noise[dataset_name]
parameters["clustering"]["evaluation"]["minimum_cluster_size"] = data.minsize[dataset_name]
parameters["clustering"]["evaluation"]["minimum_clusters"] = data.num_cluster_ranges[dataset_name][0]
parameters["clustering"]["evaluation"]["maximum_clusters"] = data.num_cluster_ranges[dataset_name][1]
print parameters["clustering"]["evaluation"]["minimum_clusters"], parameters["clustering"]["evaluation"]["maximum_clusters"]
if dataset_name in data.criteria:
parameters["clustering"]["evaluation"]["evaluation_criteria"] = data.criteria[dataset_name]
else:
parameters["clustering"]["evaluation"]["evaluation_criteria"] = data.criteria["default"]
Driver(Observer()).run(parameters)
for dataset_name in ['concentric_circles']: #data.all_datasets:
results_file = os.path.join(os.path.abspath("./tmp/%s"%dataset_name),"results/results.json")
results = convert_to_utf8(json.loads(open(results_file).read()))
@author: victor
"""
from pyproct.driver.parameters import ProtocolParameters
from pyproct.driver.driver import Driver
from pyproct.driver.observer.observer import Observer
import sys
from pyproct.driver.handlers.matrix.matrixHandler import MatrixHandler
from pyproct.tools.matrixTools import get_submatrix
from pyproct.tools.plotTools import matrixToImage
from itertools import product
import numpy
from pyproct.tools.pdbTools import get_number_of_frames
if __name__ == '__main__':
base_script = "".join(open("base_script.json","r").readlines())
parameters = ProtocolParameters.get_params_from_json(base_script)
parameters["global"]["workspace"]["base"] = sys.argv[3]
parameters["data"]["files"] = [sys.argv[1], sys.argv[2]]
frames_ini = get_number_of_frames(sys.argv[1])
frames_proto = get_number_of_frames(sys.argv[2])
print sys.argv[1],"->",frames_ini
print sys.argv[2],"->",frames_proto
try:
Driver(Observer()).run(parameters)
except SystemExit:
# Expected improductive search
# Load again the matrix
handler = MatrixHandler({
"method": "load",
if __name__ == '__main__':
parser = optparse.OptionParser(usage='%prog [--mpi] [--print] script', version=pyproct.__version__)
parser.add_option('--mpi', action="store_true", dest = "use_mpi", help="Add this flag if you want to use MPI-based scheduling.")
parser.add_option('--print', action="store_true", dest = "print_messages", help="Add this flag to print observed messages to stdout.")
options, args = parser.parse_args()
if(len(args)==0):
parser.error("You need to specify the script to be executed.")
json_script = args[0]
parameters = None
try:
parameters = ProtocolParameters.get_params_from_json(open(json_script).read())
parameters["global"]["workspace"]["base"] = os.path.abspath(parameters["global"]["workspace"]["base"])
except ValueError, e:
print "Malformed json script."
print e.message
exit()
observer = None
cmd_thread = None
if options.use_mpi:
from pyproct.driver.mpidriver import MPIDriver
from pyproct.driver.observer.MPIObserver import MPIObserver
observer = MPIObserver()
if options.print_messages:
cmd_thread = CmdLinePrinter(observer)
cmd_thread.start()
@author: victor
"""
from pyproct.driver.parameters import ProtocolParameters
from pyproct.driver.driver import Driver
from pyproct.driver.observer.observer import Observer
import sys
from pyproct.driver.handlers.matrix.matrixHandler import MatrixHandler
from pyproct.tools.matrixTools import get_submatrix
from pyproct.tools.plotTools import matrixToImage
from itertools import product
import numpy
from pyproct.tools.pdbTools import get_number_of_frames
if __name__ == '__main__':
base_script = "".join(open("base_script.json", "r").readlines())
parameters = ProtocolParameters.get_params_from_json(base_script)
parameters["global"]["workspace"]["base"] = sys.argv[3]
parameters["data"]["files"] = [sys.argv[1], sys.argv[2]]
frames_ini = get_number_of_frames(sys.argv[1])
frames_proto = get_number_of_frames(sys.argv[2])
print sys.argv[1], "->", frames_ini
print sys.argv[2], "->", frames_proto
try:
Driver(Observer()).run(parameters)
except SystemExit:
# Expected improductive search
# Load again the matrix
handler = MatrixHandler({
"method": "load",
parser.add_option(
'--print',
action="store_true",
dest="print_messages",
help="Add this flag to print observed messages to stdout.")
options, args = parser.parse_args()
if (len(args) == 0):
parser.error("You need to specify the script to be executed.")
json_script = args[0]
parameters = None
try:
parameters = ProtocolParameters.get_params_from_json(
tools.remove_comments(open(json_script).read()))
parameters["global"]["workspace"]["base"] = os.path.abspath(
parameters["global"]["workspace"]["base"])
except ValueError, e:
print "Malformed json script."
print e.message
exit()
observer = None
cmd_thread = None
if options.use_mpi:
from pyproct.driver.mpidriver import MPIDriver
from pyproct.driver.observer.MPIObserver import MPIObserver
observer = MPIObserver()
if options.print_messages:
cmd_thread = CmdLinePrinter(observer)
