def main():
parser = argparse.ArgumentParser()
parser.add_argument('-p', '--project', default='ProjectInfo.h5')
parser.add_argument('-a', '--assignments', default='Data/Assignments.h5')
args = parser.parse_args()
a = Serializer.LoadData(args.assignments)
p = Project.LoadFromHDF(args.project)
maxx, maxy, minx, miny = -np.inf, -np.inf, np.inf, np.inf
n_states = np.max(a) + 1
x = np.concatenate([p.LoadTraj(i)['XYZList'][:, 0, 0] for i in range(p['NumTrajs'])])
y = np.concatenate([p.LoadTraj(i)['XYZList'][:, 0, 1] for i in range(p['NumTrajs'])])
a = np.concatenate([a[i, :] for i in range(p['NumTrajs'])])
plot_v(minx=np.min(x), maxx=np.max(x), miny=np.min(y), maxy=np.max(y))
colors = ['b', 'r', 'm', 'c', 'g']
for j in xrange(n_states):
w = np.where(a == j)[0]
pp.scatter(x[w], y[w], marker='x', c=colors[j], label='State %d' % j,
edgecolor=colors[j], alpha=0.5)
pp.legend()
pp.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-g', '--generators', default='Data/Gens.lh5', help='Path to Gens.lh5')
parser.add_argument('-p', '--project', default='ProjectInfo.h5', help='Path to ProjectInfo.h5')
parser.add_argument('-s', '--stride', default=5, type=int, help='Stride to plot the data at')
args = parser.parse_args()
gens = Trajectory.LoadTrajectoryFile(args.generators)
gens_x = gens['XYZList'][:,0,0]
gens_y = gens['XYZList'][:,0,1]
points = np.array([gens_x, gens_y]).transpose()
tri = Delaunay(points)
PL = []
for p in points:
PL.append(Voronoi.Site(x=p[0],y=p[1]))
v,eqn,edges,wtf = Voronoi.computeVoronoiDiagram(PL)
edge_points=[]
for (l,x1,x2) in edges:
if x1>=0 and x2>=0:
edge_points.append((v[x1],v[x2]))
lines = LineCollection(edge_points, linewidths=0.5, color='k')
fig = pp.figure()
ax = fig.add_subplot(111)
fig.gca().add_collection(lines)
maxx, minx= np.max(gens_x), np.min(gens_x)
maxy, miny = np.max(gens_y), np.min(gens_y)
# plot the background
plot_v(minx=minx, maxx=maxx, miny=miny, maxy=maxy, ax=ax)
pp.xlim(minx, maxx)
pp.ylim(miny, maxy)
# plot a single trajectory
p = Project.LoadFromHDF(args.project)
t = p.LoadTraj(0)
x = t['XYZList'][:,0,0][::args.stride]
y = t['XYZList'][:,0,1][::args.stride]
cm = pp.get_cmap('spectral')
n_points = len(x)
ax.set_color_cycle([cm(1.*i/(n_points-1)) for i in range(n_points-1)])
for i in range(n_points-1):
ax.plot(x[i:i+2],y[i:i+2])
pp.title('Voronoi Microstate Decomposition, with first trajectory')
pp.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-p', '--project', default='ProjectInfo.h5')
parser.add_argument(
'-t',
'--trajectories',
nargs='+',
help='''Supply either the path to a trajectory file (i.e. Data/Gens.lh5),
or an integer, which will be interepreted as a trajectory index
into the trajectories that accompany the project. default: plot all
of the trajectories''',
default=['-1'])
args = parser.parse_args()
p = Project.LoadFromHDF(args.project)
# record the bounding box of the points so that we know
# what to render for the background
maxx, minx, maxy, miny = 1.2, -1.5, 2, -0.2
# if -1 is included, add in ALL of the trajectories
if '-1' in args.trajectories:
args.trajectories.remove('-1')
args.trajectories.extend(range(p['NumTrajs']))
# remove duplicates
args.trajectories = set(args.trajectories)
for requested in args.trajectories:
if os.path.exists(str(requested)):
traj = Trajectory.LoadTrajectoryFile(str(requested))
print 'plotting %s' % requested
markersize = 50
else:
try:
i = int(requested)
traj = p.LoadTraj(i)
print 'plotting %s' % i
markersize = 5
except ValueError:
print >> sys.stderr, 'I couldnt figure out how to deal with the argument %s' % requested
continue
except IOError as e:
print >> sys.stderr, str(e)
continue
xyz = traj['XYZList']
x = xyz[:, 0, 0]
y = xyz[:, 0, 1]
maxx, maxy = max(np.max(x), maxx), max(np.max(y), maxy)
minx, miny = min(np.min(x), minx), min(np.min(y), miny)
pp.plot(x, y, '.', markersize=markersize, alpha=0.5)
plot_v(minx=minx, maxx=maxx, miny=miny, maxy=maxy)
pp.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-p', '--project', default='ProjectInfo.h5')
parser.add_argument('-t', '--trajectories', nargs='+',
help='''Supply either the path to a trajectory file (i.e. Data/Gens.lh5),
or an integer, which will be interepreted as a trajectory index
into the trajectories that accompany the project. default: plot all
of the trajectories''', default=['-1'])
args = parser.parse_args()
p = Project.LoadFromHDF(args.project)
# record the bounding box of the points so that we know
# what to render for the background
maxx, minx, maxy, miny = 1.2, -1.5, 2, -0.2
# if -1 is included, add in ALL of the trajectories
if '-1' in args.trajectories:
args.trajectories.remove('-1')
args.trajectories.extend(range(p['NumTrajs']))
# remove duplicates
args.trajectories = set(args.trajectories)
for requested in args.trajectories:
if os.path.exists(str(requested)):
traj = Trajectory.LoadTrajectoryFile(str(requested))
print 'plotting %s' % requested
markersize = 50
else:
try:
i = int(requested)
traj = p.LoadTraj(i)
print 'plotting %s' % i
markersize=5
except ValueError:
print >> sys.stderr, 'I couldnt figure out how to deal with the argument %s' % requested
continue
except IOError as e:
print >> sys.stderr, str(e)
continue
xyz = traj['XYZList']
x = xyz[:,0,0]
y = xyz[:,0,1]
maxx, maxy = max(np.max(x), maxx), max(np.max(y), maxy)
minx, miny = min(np.min(x), minx), min(np.min(y), miny)
pp.plot(x, y, '.', markersize=markersize, alpha=0.5)
plot_v(minx=minx, maxx=maxx, miny=miny, maxy=maxy)
pp.show()
for i, fn in enumerate(traj_list):
print fn
t = np.load(fn)
c.train(t, ass[i])
#c.train(t)
C, Sigma = c.get_current_estimate()
vals, vecs = scipy.linalg.eig(C, b=Sigma)
print vals
print vecs
io.saveh(args.out, vals=vals, vecs=vecs, C=C, Sigma=Sigma)
muller.plot_v()
ref = io.loadh('ref.h5')
ref['vecs'][:,0] *= -1
vecs[:,0] *= -1
plot([0, vecs[0,0]], [0, vecs[1,0]], color='white', lw=3)
plot([0, vecs[0,1]], [0, vecs[1,1]], color='white', ls='dashed', lw=3)
plot([0, ref['vecs'][0,0]], [0, ref['vecs'][1,0]], color='red', lw=3)
plot([0, ref['vecs'][0,1]], [0, ref['vecs'][1,1]], color='red', ls='dashed', lw=3)
show()
