import rax
import numpy as np
import sys
import os
mydirname = os.path.dirname(sys.argv[0])
inroot = os.path.join(mydirname, 'relaxation-data')
traj = rax.Trajectory(0,1)
traj.set_num_gens(19)
generations = set(np.random.random_integers(19, size=(42,)))
for gen in generations:
data = np.random.random_sample(4)
print 'Adding Gen', gen, 'data', data
traj.add_generation(gen, data)
missing = traj.missing_generations()
print 'Trajectory missing generations', missing
project = rax.load_project(inroot)
# project.runs = 3
# project.clones = 2
# project.gens = 30
print 'Project missing:', list(project.missing_data())
log = ezlog.setup()
log.info('defining assign')
def assign(v, boundary=0.3):
if v <= boundary:
s = 0
else:
s = 1
return s
log.info('Setting up vars')
mydirname = os.path.dirname(sys.argv[0])
inroot = os.path.join(mydirname, 'relaxation-data')
nprocs = 2
ezlog.set_level(ezlog.INFO)
rax.setup_pool(nprocs)
log.info('Loading project')
project = rax.load_project(inroot, outputfreq=0.5)
find_states = functools.partial(assign, boundary=0.9)
p2 = project.map(find_states)
log.info('Print results')
for t in p2.get_trajectories():
print t.run, t.clone, t.get_trajectory_data()
rax.set_logging_level(logging.INFO)
# transition count matrix
N = np.zeros((len(ranges),len(ranges)), dtype=int)
# average lifetimes
T = np.zeros(len(ranges))
runs = None
clones = None
# read the trajectories in to determine the trajectory lifetimes and transition counts
processor = functools.partial(process_trajectory, ranges)
pool = rax.Pool(nprocs)
project = rax.load_project(fahroot, runs=runs, clones=clones, pool=pool, coalesce=True)
results = rax.process_trajectories(project, processor, pool=pool)
# # save the assignments
# assignments = rax.process_trajectories(project, functools.partial(assignments, ranges), pool=pool)
# np.savetxt(outfile, assignments[0], fmt='%d')
# project.savetxt('test.dat', run, clone, fmt='%f')
# sys.exit(1)
# compute lifetimes and update transition counts matrix
Ts = np.zeros(len(ranges))
for run, clone, ts, M in results:
N = N + M
for s, lifes in ts.iteritems():
