def plotFromPath(path, npy_file, y_lim=[0.5, 1]):
trans_dict = dict([("accord.npy", u"Indeks Zgodności"),
("neigh.npy", u"Korygowany Współczynnik Przekrywania")])
data_file = open(pathJoin(path, "data.txt"))
matrix = np.load(pathJoin(path, npy_file))
if npy_file == "accord.npy":
matrix = matrix[:, :20]
if npy_file == "neigh.npy":
matrix = matrix[:, :190]
means = np.mean(matrix, axis=1)
errors = np.std(matrix, axis=1)
data_dict = {}
for line in data_file:
parameter, value = line.rstrip("\n").split("\t")
data_dict[parameter] = value
plt.errorbar(np.arange(len(matrix)), means, yerr=errors)
# title_string = ("Algorithm: {algorithm}, n_iter: {n_iter},"
# "throw away: {throw_away}").format(**data_dict)
# plt.ylim(y_lim)
# plt.title(title_string)
plt.xlim(-1, len(matrix) + 1)
plt.ylabel(trans_dict[npy_file], fontsize=16)
plt.xlabel(u"Ilość skupisk", fontsize=16)
plt.tick_params(labelsize=14)
plt.xticks(np.arange(len(matrix)), eval(data_dict["list_of_cluster_n"]))
def plot_latent_old(self, filename=False):
pl.figure()
pl.clf()
pl.plot(self.training_nodes, self.training_values, "r+", ms=20)
# pl.gca().fill_between(
# self.test_nodes, self.fstar - self.s, self.fstar + self.s, color="#dddddd"
# )
pl.errorbar(
self.test_nodes,
self.fstar,
self.s,
barsabove=True,
ecolor="black",
linewidth=1,
capsize=5,
fmt="o",
)
pl.plot(self.test_nodes, self.fstar, "ro", ms=4)
# pl.plot(self.test_nodes, self.fstar, "r--", lw=2)
loglikelihood = -self.logPosterior(self.theta, self.training_nodes,
self.training_values)
# pl.title(
# "Latent Process Mean and Variance \n(length scale: %.3f , constant scale: %.3f , noise variance: %.3f )\n Log-Likelihood: %.3f"
# % (self.theta[1], self.theta[0], self.theta[2], loglikelihood)
# )
pl.title("Latent Process Mean and Variance")
pl.xlabel("nodes")
pl.ylabel("values")
if type(filename) is str:
pl.savefig(filename, bbox_inches="tight")
# pl.axis([-5, 5, -3, 3])
return self
def plot_best(self, extra=""):
b = [
x for x in self.rez['models']
if x['period'] == self.rez['best_period']
][0]
from matplotlib import pylab as plt
tt = (self.t / self.rez['best_period']) % 1
s = tt.argsort()
x = tt[s]
y = self.y[s]
z = self.dy[s]
if self.mag:
mm = where(y == max(y))
else:
mm = where(y == min(y))
pmm = x[mm]
tt = (((self.t / self.rez['best_period']) % 1.0) - pmm + 0.5) % 1.0
s = tt.argsort()
x = tt[s] - 0.5
y = self.y[s]
z = self.dy[s]
plt.errorbar(x, y, z, fmt='o', c="r")
plt.plot(b['phase'], b['f'], c="b")
plt.ylim(self.y.max() + 0.05, self.y.min() - 0.05)
plt.xlabel("phase")
plt.ylabel("flux/mag")
plt.title("Best p = %.6f (chi2 = %.3f)" %
(self.rez['best_period'], self.rez['best_chi2']))
plt.text(-0.2,
self.y.max() - 0.05,
"%s" % extra,
ha='center',
alpha=0.5)
def SNPhot_plotter_filt(obs, gp, filt=b'r'):
df = obs[obs.FLT == filt]
x = df.MJD.values
y = df.FLUXCAL.values
dy = df.FLUXCALERR.values
colors = {b'g': 'g', b'r': 'r', b'i': 'c', b'z': 'm'}
pred = pred_var = 0.
if gp is not None:
x_pred = np.linspace(x.min() - 100., x.max() + 100., 1000)
pred, pred_var = gp.predict(y, x_pred, return_var=True)
#pred, pred_cov = gp.predict(y, x_pred, return_cov=True)
pred_sig = np.sqrt(np.abs(pred_var))
plt.fill_between(x_pred,
pred - 2 * pred_sig,
pred + 2 * pred_sig,
color=colors[filt],
alpha=0.2)
plt.plot(x_pred, pred, "k", lw=1.5, alpha=0.5)
plt.ylim(
np.append(np.append(y - dy * 1.1, [0]), [pred - pred_sig]).min(),
np.append(y + dy * 1.1, [pred + pred_sig]).max())
plt.errorbar(x, y, yerr=dy, fmt=".k", capsize=0)
plt.xlim(x.min() - 30, x.max() + 30)
plt.title(filt)
return plt
def plot(self, outf=None, dosave=True, savedir="Plot/", show=True):
if outf is None:
outf = self.outf
# print outf
oo = mlab.csv2rec(outf, delimiter=" ")
# print oo
plt.errorbar(oo["time"] % self.period, oo["magnitude"], oo["error"], fmt="b.")
plt.plot(oo["time"] % self.period, oo["model"], "ro")
plt.title(
"#%i P=%f d (chisq/dof = %f) r1+r2=%f"
% (self.dotastro_id, self.period, self.outrez["chisq"], self.outrez.get("r1") + self.outrez.get("r2"))
)
ylim = plt.ylim()
# print ylim
if ylim[0] < ylim[1]:
plt.ylim(ylim[1], ylim[0])
plt.draw()
if show:
plt.show()
if dosave:
if not os.path.isdir(savedir):
os.mkdir(savedir)
plt.savefig("%splot%i.png" % (savedir, self.dotastro_id)) # ,self.period))
print("Saved", "%splot%i.png" % (savedir, self.dotastro_id)) # ,self.period)
plt.clf()
def main(root):
sims = glob(f"{root}/*/algo_stats.json")
for sim in sims:
N, T, mu, r_hgt, r_indel, r_xpose = params(rm_prefix(sim, root))
# NOTE: this is a temporary hack
if not (N == 100 and mu == 3e-4):
continue
with open(sim) as fd:
d = json.load(fd)
mus, mean_lens, sdev_lens, mean_deps, sdev_deps = [], [], [], [], []
for i, (key, val) in enumerate(d.items()):
mu, beta = coeffs(key)
x, y = np.array(val['length']), np.array(val['depth'])
mus.append(mu)
mean_lens.append(np.mean(x))
sdev_lens.append(np.std(x))
mean_deps.append(np.mean(y))
sdev_deps.append(np.std(y))
mean_lens, sdev_lens, mean_deps, sdev_deps = as_array(mean_lens, sdev_lens, mean_deps, sdev_deps)
idx = sorted(range(len(mus)), key= lambda i: mus[i])
mean_lens = mean_lens[idx]
sdev_lens = .5*sdev_lens[idx]
mean_deps = mean_deps[idx]
sdev_deps = .5*sdev_deps[idx]
plt.errorbar(mean_lens, mean_deps, xerr=sdev_lens, yerr=sdev_deps)
plt.xlabel("length")
plt.ylabel("depth")
plt.show()
def gp_regression(x, y_ave, y_std, points):
# Training set
X = np.atleast_2d(x).T
y = y_ave
dy = y_std
noise = np.random.normal(0, dy)
y += noise
# Test set
x = np.atleast_2d(np.linspace(x[0], x[-1], points)).T
kernel = C(1.0, (1e-3, 1e3)) * RBF(10, (1e-2, 1e2))
gp = GaussianProcessRegressor(kernel=kernel,
alpha=(dy / y)**2,
n_restarts_optimizer=10)
gp.fit(X, y)
y_pred, sigma = gp.predict(x, return_std=True)
if 0:
fig = plt.figure()
plt.errorbar(X, y, dy, fmt='r.', markersize=10, label=u'Observations')
plt.plot(x, y_pred, 'b-', label=u'Prediction')
plt.fill(np.concatenate([x, x[::-1]]),
np.concatenate([
y_pred - 1.9600 * sigma, (y_pred + 1.9600 * sigma)[::-1]
]),
alpha=.5,
fc='b',
ec='None',
label='95% confidence interval')
plt.xlabel('$x$')
plt.ylabel('$f(x)$')
plt.ylim(-1, 1)
plt.legend(loc='upper left')
return y_pred, sigma
def plot_hypothesis5():
weights = [
158.0, 164.2, 160.3, 159.9, 162.1, 164.6, 169.6, 167.4, 166.4, 171.0,
171.2, 172.6
]
xs = range(1, len(weights) + 1)
line = np.poly1d(np.polyfit(xs, weights, 1))
with figsize(y=2.5):
plt.figure()
plt.errorbar(range(1, 13),
weights,
label='weights',
yerr=5,
fmt='o',
capthick=2,
capsize=10)
plt.plot(xs, line(xs), c='r', label='hypothesis')
plt.xlim(0, 13)
plt.ylim(145, 185)
plt.xlabel('day')
plt.ylabel('weight (lbs)')
book_plots.show_legend()
plt.grid(False)
def errorbar_plot(data, x_spec, y_spec, fname):
""" Dynamically create errorbar plot
"""
x_label, x_func = x_spec
y_label, y_func = y_spec
# compute data
points = collections.defaultdict(list)
for syst, mat, _ in data:
x_value = x_func(syst, mat)
y_value = y_func(syst, mat)
if x_value is None or y_value is None: continue
points[x_value].append(y_value)
# plot figure
densities = []
averages = []
errbars = []
for dens, avgs in points.items():
densities.append(dens)
averages.append(np.mean(avgs))
errbars.append(np.std(avgs))
plt.errorbar(
densities, averages, yerr=errbars,
fmt='o', clip_on=False)
plt.title('')
plt.xlabel(x_label)
plt.ylabel(y_label)
plt.tight_layout()
save_figure('images/%s' % fname, bbox_inches='tight')
plt.close()
def choose_gamma_knn(X, y, range_gamma, plot_color):
'''Implement 5 fold cv to determine optimal gamma'''
#Param setup
kf = KFold(n_splits = 5)
mean_error=[]; std_error=[];
for gammaX in range_gamma:
#Params
mse_temp = []
#Set up gaussian kernel function
def gaussian_kernel(distances):
weights = np.exp(-gammaX*(distances**2))
return weights/np.sum(weights)
for train, test in kf.split(X):
#Model
model = KNeighborsRegressor(n_neighbors= len(train), weights=gaussian_kernel)
model.fit(X[train], y[train])
ypred = model.predict(X[test])
mse = mean_squared_error(y[test], ypred)
mse_temp.append(mse)
#Get mean & variance
mean_error.append(np.array(mse_temp).mean())
std_error.append(np.array(mse_temp).std())
#Plot
fig = plt.figure(figsize=(15,12))
plt.errorbar(range_gamma, mean_error, yerr=std_error, color = plot_color)
plt.xlabel('gamma')
plt.ylabel('Mean square error')
plt.title('Choice of gamma in kernelised knn - 5 fold CV')
plt.show()
def compareMassRatioVsRedshift(his, hiserr, mine, myerr, hisfield, hisid, myfield, myid, z):
import matplotlib.pylab as plt
a = []
b = []
c = []
d = []
e = []
z_list = []
for i in range(0, np.shape(mine)[0]):
if mine[i] != 0:
#his_id_idx = np.where(hisid == myid[i])[0]
pos_id_idx = np.where(hisid == myid[i])[0]
if len(pos_id_idx) == 1:
his_id_idx = int(pos_id_idx)
else:
pos_field_idx = np.where(hisfield == myfield[i])[0]
for ii in range(0, len(pos_field_idx)):
for iii in range(0, len(pos_id_idx)):
if pos_field_idx[ii] == pos_id_idx[iii]:
his_id_idx = int(pos_id_idx[iii])
#print str(myid[i]), str(myfield[i]), str(hisid[his_id_idx]), str(hisfield[his_id_idx])
assert myfield[i] == hisfield[his_id_idx]
assert myid[i] == hisid[his_id_idx]
if his[his_id_idx] != -999:
a.append(his[his_id_idx])
b.append(hiserr[his_id_idx])
c.append(mine[i])#-np.log10(((1.0+z[i]))))
d.append(myerr[i,0])#-np.log10(((1.0+z[i]))))
e.append(myerr[i,1])#-np.log10(1.0+z[i]))
z_list.append(z[i])
# since errors are just percentile, need difference from median
d = np.asarray(c)-np.asarray(d)
e = np.asarray(e)-np.asarray(c)
c_a = 10**np.array(c)
a_a = 10**np.array(a)
ratio = c_a/a_a
plt.errorbar(z_list, ratio, fmt='o',
color='b', capsize=0, alpha=0.50)
# plot the y=x line
x = np.linspace(np.min(z_list),
np.max(z_list),
10)
plt.plot(x, np.ones(len(x)), 'k--')
plt.yscale('log')
plt.xlabel("Redshift")
plt.ylabel("MCSED / Alex's [note: ratio of actual masses]")
plt.title("Redshift vs Mass Ratio (MCSED/Alex)")
#plt.legend(['With Neb. Emis.'],loc=0)#, 'W/o Neb. Emis'], loc=0)
plt.show()
def main():
# epochs == 100
bz = np.array(
[2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192, 16384])
sc = np.array([
0.97174, 0.96976, 0.96876, 0.96734, 0.96596, 0.96332, 0.95684, 0.94564,
0.93312, 0.91788, 0.90046, 0.87318, 0.82926, 0.76104
])
ec = np.array([
0.00006, 0.00034, 0.00007, 0.00012, 0.00011, 0.00040, 0.00042, 0.00040,
0.00038, 0.00040, 0.00078, 0.00086, 0.00203, 0.00591
])
# minibatches = 8192
sc0 = np.array([
0.93658, 0.94556, 0.94856, 0.94916, 0.95012, 0.94946, 0.95068, 0.95038,
0.95112, 0.95030, 0.95066, 0.95028, 0.94992, 0.94994
])
ec0 = np.array([
0.00214, 0.00078, 0.00070, 0.00115, 0.00025, 0.00028, 0.00053, 0.00041,
0.00045, 0.00023, 0.00032, 0.00058, 0.00044, 0.00022
])
plt.errorbar(bz, sc, ec, marker='o', color='red')
plt.errorbar(bz, sc0, ec0, marker='s', color='blue')
plt.xlabel("Minibatch Size")
plt.ylabel("Mean Score")
plt.tight_layout()
plt.savefig("mnist_nn_experiments_batch_size_plot.pdf",
format="pdf",
dpi=600)
plt.show()
def choose_alpha_ridge(X, y, range_C, gammaX, plot_color):
'''Implement 5 fold cv to determine optimal gamma'''
#Param setup
kf = KFold(n_splits = 5)
mean_error=[]; std_error=[];
for C in range_C:
#Params
mse_temp = []
#Model
model = KernelRidge(alpha= 1.0/(2*C), kernel= 'rbf', gamma=gammaX)
#5 fold CV
for train, test in kf.split(X):
#Model
model.fit(X[train], y[train])
ypred = model.predict(X[test])
mse = mean_squared_error(y[test], ypred)
mse_temp.append(mse)
#Get mean & variance
mean_error.append(np.array(mse_temp).mean())
std_error.append(np.array(mse_temp).std())
#Plot
fig = plt.figure(figsize=(15,12))
plt.errorbar(range_C, mean_error, yerr=std_error, color = plot_color)
plt.xlabel('C')
plt.ylabel('Mean square error')
plt.title('Choice of C in kernelised Ridge Regression - 5 fold CV, gamma = {}'.format(gammaX))
plt.show()
def transits(pipe,mode='transit-times'):
_transits = pipe.transits
if mode=='transit-times':
y = _transits.omc
yerr = _transits.ut0
ylabel = 'O - C'
if mode=='transit-rp':
y = _transits.rp
yerr = _transits.urp
ylabel = 'Rp/Rstar'
x = _transits.transit_id
xl = x.min() -1, x.max() + 1
xlabel = 'transit-id'
yspan = y.ptp()
yl = y.min() - 1 * yspan, y.max() + 1 * yspan
plt.errorbar(x, y, yerr=yerr, fmt='o', ms=5, mew=0, capsize=0)
plt.xlim(*xl)
plt.ylim(*yl)
plt.xlabel(xlabel)
plt.ylabel(ylabel)
AddAnchored(mode,prop=tprop,frameon=True,loc=2)
def extractEffectiveMass(df,cut_low=0,cut_right=None,n_cuts=5,makePlot=False):
if cut_right==None:
cut_right=max(df["t"])
window=(cut_right-cut_low)/n_cuts
slope=np.zeros(n_cuts)
intercept=np.zeros(n_cuts)
slopeError=np.zeros(n_cuts)
interceptError=np.zeros(n_cuts)
for i in range(0,n_cuts):
# select the right intervals for the linear fit
cut_low_current=cut_low + i*window
cut_high_current=cut_low + (i+1)*window
df1=df[(df["t"]>cut_low_current) & (df["t"]<cut_high_current) ]
if len(df1["t"]) <= 3:
raise not_enough_data()
params,covs=curve_fit(linear,df1["t"],df1["W"],sigma=df1["deltaW"],maxfev=100000)
slope[i]=params[0]
intercept[i]=params[1]
slopeError[i]=sqrt(covs[0][0])
interceptError[i]=sqrt(covs[1][1])
if makePlot==True:
up=(slope[i]+slopeError[i])+(intercept[i]+interceptError[i])/df1["t"]
down=(slope[i]-slopeError[i])+(intercept[i]-interceptError[i])/df1["t"]
plt.fill_between(df1["t"],up,down,alpha=0.4)
plt.errorbar(np.array(df1["t"]),np.array(df1["W"])/np.array(df1["t"]),np.array(df1["deltaW"])/np.array(df1["t"]),fmt="or")
return np.array([slope.mean(),sqrt( slopeError.mean()**2 + slope.var())])
def parse_error(d):
if not np.isfinite(d.fp_local):
return
f = ais_code.fp_to_ne(d.fp_local)
f0 = ais_code.fp_to_ne(d.fp_local + d.fp_local_error)
f1 = ais_code.fp_to_ne(d.fp_local - d.fp_local_error)
if errors:
plt.plot((d.time, d.time),(f0,f1),
color='lightgrey', linestyle='solid',
marker='None', zorder=-1000,**kwargs)
plt.plot(d.time, f, fmt, ms=self.marker_size, zorder=1000, **kwargs)
if full_marsis and hasattr(d, 'maximum_fp_local'):
plt.plot(d.time, ais_code.fp_to_ne(d.maximum_fp_local),
'b.', ms=self.marker_size, zorder=900, **kwargs)
if full_marsis:
if np.isfinite(d.morphology_fp_local):
v, e = ais_code.fp_to_ne(d.morphology_fp_local,
d.morphology_fp_local_error)
plt.errorbar(float(d.time), v, yerr=e,
marker='x', ms=1.3, color='purple',
zorder=1e90, capsize=0., ecolor='plum')
if np.isfinite(d.integrated_fp_local):
v, e = ais_code.fp_to_ne(d.integrated_fp_local,
d.integrated_fp_local_error)
plt.errorbar(float(d.time), v, yerr=e,
marker='x', ms=1.3, color='blue',
zorder=1e99, capsize=0., ecolor='cyan')
def plot_source_radius(cat):
mw = []
mw_std = []
source_radius = []
source_radius_std = []
plt.figure(figsize=(10, 4.5))
# Read the source radius.
for event in cat:
mag = event.magnitudes[1]
if len(mag.comments) != 2:
continue
mw.append(mag.mag)
mw_std.append(mag.mag_errors.uncertainty)
sr, std = mag.comments[1].text.split(";")
_, sr = sr.split("=")
_, std = std.split("=")
sr = float(sr[:-1])
std = float(std)
source_radius.append(sr)
source_radius_std.append(std)
plt.errorbar(mw, source_radius, yerr=source_radius_std,
fmt="o", linestyle="None")
plt.xlabel("Mw", fontsize="x-large")
plt.ylabel("Source Radius [m]", fontsize="x-large")
plt.grid()
plt.savefig("/Users/lion/Desktop/SourceRadius.pdf")
def plotting_multiple_files(dict_of_files, title='Title', check='F'):
linestyles = {'fil': '--', 'raw': '-', 'vic': '-'}
for reps in sorted(list(dict_of_files)):
Sample_Type = reps.split(' ')[0]
if not isinstance(dict_of_files[reps], pd.DataFrame):
df = pd.read_csv(dict_of_files[reps], skiprows=0, delimiter='\t')
else:
df = dict_of_files[reps]
df.reset_index(inplace=True, drop=False)
df.rename(columns={
'c_mean': 'mean',
'a_mean': 'mean',
'c_std': 'std',
'a_std': 'std'
},
inplace=True)
plt.plot('wl',
'mean',
data=df,
label=reps,
linestyle=linestyles[Sample_Type])
plt.errorbar('wl',
'mean',
yerr='std',
fmt='k-',
linewidth=0.5,
data=df)
plt.ylabel('[1/m]')
plt.xlabel('Wavelength (nm)')
plt.title(title)
plt.legend(sorted(list(dict_of_files)))
return plt
def check_model(self):
gamma11, M11, N11 = map(
lambda v: (v[1], v[2] - v[1], v[1] - v[0]),
zip(*np.percentile(self.samples, [16, 50, 84], axis=0)))
means = [gamma11[0], M11[0], N11[0]]
ups = [gamma11[1], M11[1], N11[1]]
downs = [gamma11[2], M11[2], N11[2]]
print(means, ups, downs)
dict_obs = self.load()
dict_SMHM = dict(gamma10=0.57, gamma11= gamma11[0], beta10=None, beta11=None,\
M10=11.95, SHMnorm10=None, M11=M11[0], SHMnorm11=N11[0])
maker = make_satellites_only(use_peak=True, use_Multidark=False)
df_sat = maker.make_sat(dict_SMHM=dict_SMHM,
Mstar_low=11.2,
Mstar_up=12,
mu=2.5,
AK=0.013,
sigmaK=0.1,
M0=1.5)
bins = np.append(dict_obs['rbins'] - dict_obs['rbinwidth'] / 2,
dict_obs['rbins'][-1] +
dict_obs['rbinwidth'] / 2) #restore original bins
Vol = (250 / 0.7)**3
model = np.histogram(df_sat['Re_sat'],
bins=bins)[0] / Vol / dict_obs['rbinwidth']
plt.errorbar(dict_obs['rbins'],
dict_obs['phi'],
yerr=dict_obs['err'],
label='SDSS sat',
markersize=15,
color='navy',
fmt='v',
zorder=1)
plt.plot(dict_obs['rbins'],
model,
lw=4,
label='satellites, MCMC',
color='navy',
ls='-',
zorder=2)
plt.yscale('log')
plt.ylabel('$\phi(R_e)$')
plt.xlabel('$\log{R_e} \ [kpc]$')
plt.xlim(0.25, 2.5)
plt.ylim(3.e-9, 5.e-4)
#plt.ylim(5.e-9,1.e-4)
plt.legend(frameon=False, fontsize=30)
plt.title('Evolving SMHM, MQGs')
plt.savefig('./Pictures/modelMCMC.pdf', bbox_inches='tight')
plt.close()
def plot(self, outf=None, dosave=True, savedir="Plot/", show=True):
if outf is None:
outf = self.outf
#print outf
oo = mlab.csv2rec(outf, delimiter=" ")
#print oo
plt.errorbar(oo['time'] % self.period,
oo['magnitude'],
oo['error'],
fmt="b.")
plt.plot(oo['time'] % self.period, oo['model'], "ro")
plt.title("#%i P=%f d (chisq/dof = %f) r1+r2=%f" % (self.dotastro_id,self.period,self.outrez['chisq'],\
self.outrez.get('r1') + self.outrez.get('r2')))
ylim = plt.ylim()
#print ylim
if ylim[0] < ylim[1]:
plt.ylim(ylim[1], ylim[0])
plt.draw()
if show:
plt.show()
if dosave:
if not os.path.isdir(savedir):
os.mkdir(savedir)
plt.savefig("%splot%i.png" %
(savedir, self.dotastro_id)) #,self.period))
print "Saved", "%splot%i.png" % (savedir, self.dotastro_id
) #,self.period)
plt.clf()
def get_fitting_isochrone(self, isochrone_fitter, ax=None,
spectrum_ids=[0,1]):
combined_stellar_params = self.get_combined_stellar_parameters(
spectrum_ids=spectrum_ids)
(age, metallicity), closest_isochrone = \
isochrone_fitter.find_closest_isochrone(
teff=combined_stellar_params['teff'],
logg=combined_stellar_params['logg'],
feh=combined_stellar_params['feh'])
if ax is None:
return closest_isochrone
else:
ax.plot(closest_isochrone['teff'], closest_isochrone['logg'])
ax.errorbar([combined_stellar_params['teff']],
[combined_stellar_params['logg']],
xerr=[combined_stellar_params['teff_uncertainty']],
yerr=[combined_stellar_params['logg_uncertainty']],
label='Teff={0:.2f}+-{1:.2f}\n logg={2:.2f}+-{3:.2f}'
.format(combined_stellar_params['teff'],
combined_stellar_params['teff_uncertainty'],
combined_stellar_params['logg'],
combined_stellar_params['logg_uncertainty']))
ax.set_title('Age = {0:.2g} Gyr [Fe/H] = {1:.2g}'.format(age, metallicity))
ax.invert_xaxis()
ax.invert_yaxis()
def do_plot_obs(self):
""" Plot the observed radial velocities as a function of time.
Data from each file are color coded and labeled.
"""
# import pyqtgraph as pg
colors = 'bgrcmykw' # lets hope for less than 9 data-sets
t, rv, err = self.time, self.vrad, self.error # temporaries
plt.figure()
# p = pg.plot()
# plot each files' values
for i, (fname, [n, nout]) in enumerate(sorted(self.provenance.iteritems())):
m = n-nout # how many values are there after restriction
# e = pg.ErrorBarItem(x=t[:m], y=rv[:m], \
# height=err[:m], beam=0.5,\
# pen=pg.mkPen(None))
# pen={'color': 0.8, 'width': 2})
# p.addItem(e)
# p.plot(t[:m], rv[:m], symbol='o')
plt.errorbar(t[:m], rv[:m], yerr=err[:m], \
fmt='o'+colors[i], label=fname)
t, rv, err = t[m:], rv[m:], err[m:]
plt.xlabel('Time [days]')
plt.ylabel('RV [km/s]')
plt.legend()
plt.tight_layout()
plt.show()
def display_vecstascollector_summary(stcol):
n = stcol.getStat("N[0]")
print n
mean = stcol.getMean()
stddev = stcol.getStdDev()
ucov = (1.0 / n) * stcol.getXtX()
cov = stcol.getCovariance()
corr = stcol.getCorrelation()
pxy_px_py = ucov - outer(mean, mean)
plt.subplot(4, 2, 1)
plt.errorbar(arange(len(mean)), mean, yerr=stddev)
plt.title("activations mean and stddev")
plt.subplot(4, 2, 2)
plot_histogram(mean, "activations mean")
plt.subplot(4, 2, 3)
plot_offdiag_histogram(ucov, "uncentered covariances")
plt.subplot(4, 2, 4)
plot_diag_histogram(ucov, "uncentered variances")
plt.subplot(4, 2, 5)
plot_offdiag_histogram(cov, "covariances")
plt.subplot(4, 2, 6)
plot_diag_histogram(cov, "variances")
plt.subplot(4, 2, 7)
plot_offdiag_histogram(corr, "correlations")
plt.subplot(4, 2, 8)
plot_histogram(stddev, "stddevs")
plt.show()
def plot(scores, scores2=None):
import matplotlib.pylab as pl
from matplotlib.ticker import FuncFormatter
def percentages(x, pos=0):
return "%2.2f%%" % (100 * x)
ax1 = pl.subplot(211)
pl.errorbar(scores2[:, 1], scores2[:, 2], yerr=scores2[:, 5], c="k", marker="o")
# if scores2 is not None:
# pl.errorbar(scores2[:, 1] + 0.02, scores2[:, 2], yerr=scores2[:, 5],
# c='0.5', marker='s')
pl.ylabel("Singular acc.")
ax1.yaxis.set_major_formatter(FuncFormatter(percentages))
pl.xlabel("Proportion of training set used")
ax2 = pl.subplot(212, sharex=ax1)
pl.errorbar(scores[:, 1], scores[:, 3], yerr=scores[:, 6], c="k", marker="o")
if scores2 is not None:
pl.errorbar(scores2[:, 1], scores2[:, 3], yerr=scores2[:, 6], c="k", marker="s")
ax2.yaxis.set_major_formatter(FuncFormatter(percentages))
# ax3 = pl.subplot(313, sharex=ax2)
pl.errorbar(scores[:, 1] + 0.02, scores[:, 4], yerr=scores[:, 7], c="0.5", marker="o")
if scores2 is not None:
pl.errorbar(scores2[:, 1] + 0.02, scores2[:, 4], yerr=scores2[:, 7], c="0.5", marker="s")
pl.ylabel("Plural and combined acc.")
# ax3.yaxis.set_major_formatter(FuncFormatter(percentages))
# pl.setp(ax3.get_xticklabels(), visible=False)
# pl.show()
for ext in ("pdf", "svg", "png"):
pl.savefig("train_size-i.%s" % ext)
def display_vecstascollector_summary(stcol):
n = stcol.getStat("N[0]")
print n
mean = stcol.getMean()
stddev = stcol.getStdDev()
ucov = (1.0/n)*stcol.getXtX()
cov = stcol.getCovariance()
corr = stcol.getCorrelation()
pxy_px_py = ucov-outer(mean,mean)
plt.subplot(4,2,1)
plt.errorbar(arange(len(mean)),mean,yerr=stddev)
plt.title("activations mean and stddev")
plt.subplot(4,2,2)
plot_histogram(mean, "activations mean")
plt.subplot(4,2,3)
plot_offdiag_histogram(ucov, "uncentered covariances")
plt.subplot(4,2,4)
plot_diag_histogram(ucov, "uncentered variances")
plt.subplot(4,2,5)
plot_offdiag_histogram(cov, "covariances")
plt.subplot(4,2,6)
plot_diag_histogram(cov, "variances")
plt.subplot(4,2,7)
plot_offdiag_histogram(corr, "correlations")
plt.subplot(4,2,8)
plot_histogram(stddev, "stddevs")
plt.show()
def plot_avg(measure_type, tofile=None):
fig,ax = plt.subplots()
for name in system_names:
Y = []
syst, fmt = systems[name]
for op in op_types:
if measure_type == 'latency':
latencies = get_datapoints_latency(op)
Y_op, _ = latencies[name]
elif measure_type == 'throughput':
throughputs = get_datapoints_throughput(op)
Y_op = throughputs[name]
Y.append(Y_op)
Y = np.mean(Y, axis=0)
plt.errorbar(X,Y,fmt=fmt,label=name)
ax.set_xticks(X)
ax.set_xlabel('Number of concurrent nodes.')
ax.set_xlim([0,17])
if measure_type == 'throughput':
ax.set_ylabel('Average throughput in KOps per second.')
elif measure_type == 'latency':
ax.set_ylabel('Average latency in ms.')
lgd = plt.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3,
ncol=4, mode="expand", borderaxespad=0.)
plt.grid(True)
if tofile is not None:
plt.savefig(tofile, bbox_extra_artists=(lgd,), bbox_inches='tight')
else:
plt.show()
def plot_latent(self, filename=False):
pl.figure(figsize=[15, 9])
pl.clf()
errorbar_df = self.df.iloc[list(
self.test_nodes)].sort_values(by=["pvtdist"])
pl.errorbar(
errorbar_df["pvtdist"].values,
errorbar_df["fstar"].values,
errorbar_df["variance_s"].values,
barsabove=True,
ecolor="black",
linewidth=1,
capsize=5,
fmt="o",
)
plot_df = self.df.iloc[list(
self.training_nodes)].sort_values(by=["pvtdist"])
pl.plot(plot_df["pvtdist"].values,
plot_df["train_vals"].values,
"r+",
ms=20)
if self.pivot_flag == True:
pvt_dist_df = self.df.sort_values(by=["pvtdist"])
pl.plot(pvt_dist_df["pvtdist"].values,
pvt_dist_df["pvtdist"].values)
pl.title("Latent Process Mean and Variance")
pl.xlabel("pivot distance")
pl.ylabel("values")
if type(filename) is str:
pl.savefig(filename, bbox_inches="tight")
# pl.axis([-5, 5, -3, 3])
return self
def errorbar_plot(data, x_spec, y_spec, fname):
""" Dynamically create errorbar plot
"""
x_label, x_func = x_spec
y_label, y_func = y_spec
# compute data
points = collections.defaultdict(list)
for syst, mat, _ in data:
x_value = x_func(syst, mat)
y_value = y_func(syst, mat)
if x_value is None or y_value is None: continue
points[x_value].append(y_value)
# plot figure
densities = []
averages = []
errbars = []
for dens, avgs in points.items():
densities.append(dens)
averages.append(np.mean(avgs))
errbars.append(np.std(avgs))
plt.errorbar(densities, averages, yerr=errbars, fmt='o', clip_on=False)
plt.title('')
plt.xlabel(x_label)
plt.ylabel(y_label)
plt.tight_layout()
save_figure('images/%s' % fname, bbox_inches='tight')
plt.close()
def plot_runs(runs):
""" Plot population evolutions
"""
ts = range(len(runs[0]))
cmap = plt.get_cmap('viridis')
for i, r in enumerate(runs):
mean, var = zip(*r)
bm, cm = zip(*mean)
bv, cv = zip(*var)
color = cmap(float(i)/len(runs))
plt.errorbar(ts, bm, fmt='-', yerr=bv, c=color)
plt.errorbar(ts, cm, fmt='--', yerr=cv, c=color)
plt.title('population evolution overview')
plt.xlabel('time')
plt.ylabel('value')
plt.ylim((0, 1))
plt.plot(0, 0, '-', c='black', label='benefit value')
plt.plot(0, 0, '--', c='black', label='cost value')
plt.legend(loc='best')
plt.savefig('result.pdf')
plt.show()
def plot_energy_curve(y_min, y_eb, mit_min, mit_eb, error_mit=False):
fig = plt.figure(0)
plt.plot(r_values, energies) # Theory curve
error_labels = ['Total duration = 1,700 ns', 'Total duration = 2,740 ns']
for j in range(len(y_min)):
plt.errorbar(r_values,
y_min[j],
marker='o',
markersize=1,
linestyle='None',
yerr=y_eb[j],
label=error_labels[j])
if error_mit:
plt.errorbar(r_values,
mit_min,
marker='o',
markersize=1,
linestyle='None',
yerr=mit_eb,
label="Error mitigated result")
plt.legend()
plt.xlabel(r'Bond distance (Angstrom)', fontsize=20)
plt.ylabel(r'Total Energy (Hatree)', fontsize=20)
plt.show()
def plot_source_radius(cat):
mw = []
mw_std = []
source_radius = []
source_radius_std = []
plt.figure(figsize=(10, 4.5))
# Read the source radius.
for event in cat:
mag = event.magnitudes[1]
if len(mag.comments) != 2:
continue
mw.append(mag.mag)
mw_std.append(mag.mag_errors.uncertainty)
sr, std = mag.comments[1].text.split(";")
_, sr = sr.split("=")
_, std = std.split("=")
sr = float(sr[:-1])
std = float(std)
source_radius.append(sr)
source_radius_std.append(std)
plt.errorbar(mw, source_radius, yerr=source_radius_std,
fmt="o", linestyle="None")
plt.xlabel("Mw", fontsize="x-large")
plt.ylabel("Source Radius [m]", fontsize="x-large")
plt.grid()
plt.savefig("/Users/lion/Desktop/SourceRadius.pdf")
def main():
parser = OptionParser(description='Fitting to a noisy data generated by a known function')
parser.add_option("--npoints", type="int", help="number of data points")
parser.add_option("--low", type="float", help="smallest data point")
parser.add_option("--high", type="float", help="highest data point")
parser.add_option("--sigma", type="float", help="std of noise")
(options, args) = parser.parse_args()
pl.figure(1,(7,6))
ax = pl.subplot(1,1,1)
pl.connect('key_press_event',kevent.press)
sigma = options.sigma
Ls = np.append(np.linspace(options.low,options.high,options.npoints),46)
nLs = np.linspace(min(Ls),max(Ls),100)
Mis = HalfLog(Ls,.5,0.5)
errs = np.random.normal(0,sigma, len(Mis))
Mis = Mis+errs
pl.errorbar(Ls,Mis,errs,ls='',marker='s',color='b')
print sigma/Mis
coeff, var_matrix = curve_fit(FreeLog,Ls,Mis,(1.0,1.0,1.0))
err = np.sqrt(np.diagonal(var_matrix))
dof = len(Ls) - len(coeff)
chisq = sum(((Mis-FreeLog(Ls,coeff[0],coeff[1],coeff[2]))/sigma)**2)
cdf = special.chdtrc(dof,chisq)
print 'Free: a = %0.2f(%0.2f); b = %0.2f(%0.2f); c = %0.2f(%0.2f); p-value = %0.2f ' %(coeff[0],err[0],coeff[1],err[1],coeff[2],err[2],cdf)
pl.plot(nLs,FreeLog(nLs,coeff[0],coeff[1],coeff[2]),label='Free',color='y')
coeff, var_matrix = curve_fit(ZeroLog,Ls,Mis,(1.0,1.0))
err = np.sqrt(np.diagonal(var_matrix))
dof = len(Ls) - len(coeff)
chisq = sum(((Mis-ZeroLog(Ls,coeff[0],coeff[1]))/sigma)**2)
cdf = special.chdtrc(dof,chisq)
print 'Zero: a = %0.2f(%0.2f); c = %0.2f(%0.2f); p-value = %0.2f' %(coeff[0],err[0],coeff[1],err[1],cdf)
pl.plot(nLs,ZeroLog(nLs,coeff[0],coeff[1]),label='Zero',color='g')
pl.tight_layout()
coeff, var_matrix = curve_fit(HalfLog,Ls,Mis,(1.0,1.0))
err = np.sqrt(np.diagonal(var_matrix))
dof = len(Ls) - len(coeff)
chisq = sum(((Mis-HalfLog(Ls,coeff[0],coeff[1]))/sigma)**2)
cdf = special.chdtrc(dof,chisq)
print 'Half: a = %0.2f(%0.2f); c = %0.2f(%0.2f); p-value = %0.2f' %(coeff[0],err[0],coeff[1],err[1],cdf)
pl.plot(nLs,HalfLog(nLs,coeff[0],coeff[1]),label='Half',color='b')
pl.tight_layout()
coeff, var_matrix = curve_fit(OneLog,Ls,Mis,(1.0,1.0))
err = np.sqrt(np.diagonal(var_matrix))
dof = len(Ls) - len(coeff)
chisq = sum(((Mis-OneLog(Ls,coeff[0],coeff[1]))/sigma)**2)
cdf = special.chdtrc(dof,chisq)
print 'Unity: a = %0.2f(%0.2f); c = %0.2f(%0.2f); p-value = %0.2f' %(coeff[0],err[0],coeff[1],err[1],cdf)
pl.plot(nLs,OneLog(nLs,coeff[0],coeff[1]),label='Unity',color='r')
pl.tight_layout()
pl.legend()
pl.show()
def stellar_distribution_plot(frame, fit):
# Plot the data and model
plt.errorbar(frame["bins"], frame["bin_count"], xerr=frame["bins_error"], yerr=frame["count_error"], fmt="o", ms=0.5, color="black", ecolor="grey", elinewidth=0.25, label="Gaia DR2", zorder=1)
# Density distribution model
summation_s_0 = frame["bin_count"].values.max()
l_c, r_b = 3, 2.5
xb = np.linspace(0, 16, 50)
yb = (summation_s_0 * l_c)/np.sqrt(((xb - r_b) ** 2) + (l_c ** 2))
xp = np.array([frame['bins'].iloc[0], frame['bins'].iloc[14], frame['bins'].iloc[-1]])
yp = np.array([frame['bin_count'].iloc[0], frame['bin_count'].iloc[14], frame['bin_count'].iloc[-1]])
params = fix_points(fit, xb, yb, xp, yp)
ppoly = np.polynomial.Polynomial(params)
pdata = np.linspace(0, 16, 50)
plt.plot(pdata, ppoly(pdata), ms=1, color="blue", label="Best fit density distribution model", zorder=2)
# Plot characteristics
plt.title("Stellar Density Distribution")
plt.legend(loc="upper right")
plt.xlabel("Galactic radius ($kpc$)")
plt.ylabel("Density distribution ($arbitrary$ $units$)")
plt.xlim(0, 16) # Adjustment for galactic radius
plt.ylim(0, frame["bin_count"].values.max() + (1/10 * frame["bin_count"].values.max()))
plt.show()
# Stellar disc model against observational data (Gaia)
return
def nova_plot():
erg2mev=624151.
fig=plot.figure()
yrange = [1e-6,2e-4]
xrange = [1e-1,1e5]
plot.fill_between([0.2,10e3],[yrange[1],yrange[1]],[yrange[0],yrange[0]],facecolor='yellow',interpolate=True,color='yellow',alpha=0.5)
plot.annotate('AMEGO',xy=(3,9e-5),xycoords='data',fontsize=26,color='black')
lat=ascii.read("data/NMon2012.LAT.dat",names=['energy','en_low','en_high','flux','flux_err','tmp'])
plot.scatter(lat['energy'],lat['flux']*erg2mev,color='red')
plot.errorbar(lat['energy'],lat['flux']*erg2mev,xerr=[lat['en_low'],lat['en_high']],yerr=lat['flux_err']*erg2mev,ecolor='red',capsize=0,fmt='none')
latul=ascii.read("data/NMon2012.LAT.limits.dat",names=['energy','en_low','en_high','flux','tmp1','tmp2','tmp3','tmp4'])
plot.errorbar(latul['energy'],latul['flux']*erg2mev,xerr=[latul['en_low'],latul['en_high']],yerr=0.5*latul['flux']*erg2mev,uplims=True,ecolor='red',capsize=0,fmt='none')
plot.scatter(latul['energy'],latul['flux']*erg2mev,color='red')
leptonic=ascii.read("data/sp-NMon12-IC-best-fit-1MeV-30GeV.txt",names=['energy','flux'],data_start=1)
hadronic=ascii.read("data/sp-NMon12-pi0-and-secondaries.txt",names=['energy','flux1','flux2'],data_start=1)
plot.plot(leptonic['energy'],leptonic['flux']*erg2mev,'r--',color='black',lw=2,label='Leptonic')
plot.plot(hadronic['energy'],hadronic['flux2']*erg2mev,color='black',lw=2,label='Hadronic+Secondary Leptons')
plot.legend(loc='upper right',fontsize='small',frameon=False,framealpha=0.5)
plot.xscale('log')
plot.yscale('log')
plot.ylim(yrange)
plot.xlim(xrange)
plot.xlabel(r'Energy (MeV)')
plot.ylabel(r'Energy$^2 \times $ Flux (Energy) (erg cm$^{-2}$ s$^{-1}$)')
plot.title('Nova V339 Del 2013')
plot.savefig('Nova_SED.png', bbox_inches='tight')
plot.savefig('Nova_SED.eps', bbox_inches='tight')
plot.show()
plot.close()
def process_mmd_experiment(width_class):
results_file_name = mmd_experiment.results_file_stub + "_" + width_class + ".pickle"
results = pickle.load( open(results_file_name,'rb' ) )
callibration_mmds = np.loadtxt('results/callibration_mmds.csv')
mean_callibration = np.mean(callibration_mmds)
mmd_squareds = results['mmd_squareds']
hidden_layer_numbers = results['hidden_layer_numbers']
hidden_unit_numbers = results['hidden_unit_numbers']
num_repeats = mmd_squareds.shape[2]
mean_mmds = np.mean( mmd_squareds, axis = 2 )
std_mmds = np.std( mmd_squareds, axis = 2 ) / np.sqrt(num_repeats)
plt.figure()
for hidden_layer_number, index in zip(hidden_layer_numbers,range(len(hidden_layer_numbers))):
if hidden_layer_number==1:
layer_string = ' hidden layer'
else:
layer_string = ' hidden layers'
line_name = str(hidden_layer_number) + layer_string
plt.errorbar( hidden_unit_numbers, mean_mmds[:,index], yerr = 2.*std_mmds[:,index], label = line_name)
plt.xlabel('Number of hidden units per layer')
plt.xlim([0,60])
plt.ylabel('MMD SQUARED(GP, NN)')
plt.ylim([0.,0.02])
plt.axhline(y=mean_callibration, color='r', linestyle='--')
plt.legend()
output_file_name = "../figures/mmds_" + width_class + ".pdf"
plt.savefig(output_file_name)
embed()
plt.show()
def sanity_2dCircularFit(self):
import numpy as np
import matplotlib.pylab as plt
from PyAstronomy import funcFit as fuf
# Get the circular model and assign
# parameter values
c = fuf.Circle2d()
c["r"] = 1.0
c["t0"] = 0.0
c["per"] = 3.0
# Evaluate the model at a number of
# time stamps
t = np.linspace(0.0, 10.0, 20)
pos = c.evaluate(t)
# Add some error to the "measurement"
pos += np.reshape(np.random.normal(0.0, 0.2, pos.size), pos.shape)
err = np.reshape(np.ones(pos.size), pos.shape) * 0.2
# Define free parameters and fit the model
c.thaw(["r", "t0", "per"])
c.fit(t, pos, yerr=err)
c.parameterSummary()
# Evaluate the model at a larger number of
# points for plotting
tt = np.linspace(0.0, 10.0, 200)
model = c.evaluate(tt)
# Plot the result
plt.errorbar(pos[::,0], pos[::,1], yerr=err[::,1], \
xerr=err[::,0], fmt='bp')
plt.plot(model[::,0], model[::,1], 'r--')
def plotRocCurves(file_legend):
pylab.clf()
pylab.figure(1)
pylab.xlabel('1 - Specificity', fontsize=12)
pylab.ylabel('Sensitivity', fontsize=12)
pylab.title("Need for Referral")
pylab.grid(True, which='both')
pylab.xticks([i/10.0 for i in range(1,11)])
pylab.yticks([i/10.0 for i in range(0,11)])
pylab.tick_params(axis="both", labelsize=15)
for file, legend in file_legend:
points = open(file,"rb").readlines()
x = [float(p.split()[0]) for p in points]
y = [float(p.split()[1]) for p in points]
dev = [float(p.split()[2]) for p in points]
x = [0.0] + x
y = [0.0] + y
dev = [0.0] + dev
auc = np.trapz(y, x) * 100
aucDev = np.trapz(dev, x) * 100
pylab.grid()
pylab.errorbar(x, y, yerr = dev, fmt='-')
pylab.plot(x, y, '-', linewidth = 1.5, label = legend + u" (AUC = {0:0.1f}% \xb1 {1:0.1f}%)".format(auc,aucDev))
pylab.legend(loc = 4, borderaxespad=0.4, prop={'size':12})
pylab.savefig("referral/referral-curves.pdf", format='pdf')
def sanity_example_binningx0dt_example2(self):
"""
Checking `binningx0dt` example 2.
"""
import numpy as np
import matplotlib.pylab as plt
from PyAstronomy.pyasl import binningx0dt
# Generate some data
x = np.arange(-100,999)
# Create some holes in the data
x = np.delete(x, range(340,490))
x = np.delete(x, range(670,685))
x = np.delete(x, range(771,779))
y = np.sin(x/100.)
y += np.random.normal(0,0.1,len(x))
# Bin using bin width of 27 and starting at minimum x-value.
# Use beginning of bin as starting value.
r1, dt1 = binningx0dt(x, y, dt=27, x0=min(x), useBinCenter=True)
# As previously, but use the mean x-value in the bins to produce the
# rebinned time axis.
r2, dt2 = binningx0dt(x, y, dt=27, x0=min(x), useMeanX=True)
print "Median shift between the time axes: ", np.median(r1[::,0] - r2[::,0])
print " -> Time bins are not aligned due to 'forced' positioning of"
print " the first axis."
# Plot the output
plt.plot(x,y, 'b.-')
plt.errorbar(r1[::,0], r1[::,1], yerr=r1[::,2], fmt='kp--')
plt.errorbar(r2[::,0], r2[::,1], yerr=r2[::,2], fmt='rp--')
def method_errorbar(data,xlabels, line_color=default_color,
med_color=None, legend=None, y_offset=0.0,alpha=0.05):
if not med_color:
med_color=line_color
ax.grid(axis='x', color='0.9', linestyle='-', linewidth=0.2)
ax.set_axisbelow(True)
n,m=data.shape
medians = [percentile(data[:,i],50) for i in range(m)]
xerr = [[ medians[i]-percentile(data[:,i],100*(alpha/2.)),
percentile(data[:,i],100*(1-alpha/2.))-medians[i] ]
for i in range(m)]
xerr=np.array(xerr).transpose()
y_marks = np.array(range(len(xlabels)))-y_offset
plt.errorbar(y=y_marks,
x=medians,xerr=xerr,fmt='|',capsize=0,color=line_color,
ecolor=line_color,elinewidth=0.3,markersize=2)
plt.xlabel('% cases used', fontsize=8)
ax.tick_params(axis='x', which='both', labelsize=8)
ax.set_yticks(np.array(range(len(xlabels))))
ax.set_yticklabels(xlabels,fontsize=6)
plt.ylim((min(y_marks)-0.5,max(y_marks)+0.5))
spines_to_remove = ['top', 'right','left']
for spine in spines_to_remove:
ax.spines[spine].set_visible(False)
ppl.utils.remove_chartjunk(ax, ['top', 'right', 'bottom'], show_ticks=False)
if legend:
rect = legend.get_frame()
rect.set_facecolor(light_grey)
rect.set_linewidth(0.0)
def plot_table(*positional_parameters,errorbars=None,xrange=None,yrange=None,
title="",xtitle="",ytitle="",show=1,legend=None,color=None):
n_arguments = len(positional_parameters)
if n_arguments == 0:
return
fig = plt.figure()
if n_arguments == 1:
y = positional_parameters[0]
x = np.arange(y.size)
plt.plot(x,y,label=legend)
elif n_arguments == 2:
x = positional_parameters[0]
y = positional_parameters[1]
if len(y.shape) == 1:
y = np.reshape(y,(1,y.size))
if isinstance(legend,str):
legend = [legend]
if isinstance(color,str):
color = [color]
for i in range(y.shape[0]):
if legend is None:
ilegend = None
else:
ilegend = legend[i]
if color is None:
icolor = None
else:
icolor = color[i]
if errorbars is None:
plt.plot(x,y[i],label=ilegend,color=icolor)
else:
plt.errorbar(x,y[i],yerr=errorbars[i],label=ilegend,color=icolor)
else:
raise Exception("Incorrect number of arguments")
plt.xlim( xrange )
plt.ylim( yrange )
if legend is not None:
ax = plt.subplot(111)
ax.legend(bbox_to_anchor=(1.1, 1.05))
plt.title(title)
plt.xlabel(xtitle)
plt.ylabel(ytitle)
if show:
plt.show()
return fig
def main():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('losses', nargs='+', type=str)
parser.add_argument('-o', '--output', default='log-loss', type=str)
#parser.add_argument('--dataset', default='Test', type=str)
parser.add_argument('--captions', nargs='+', type=str)
args = parser.parse_args()
rs = np.random.RandomState(0)
vz = VzLog(args.output)
plt.figure()
for i, loss_fn in enumerate(args.losses):
print('file', loss_fn)
data = dd.io.load(loss_fn)
iter = data['iterations'][0]
losses = data['losses'].mean(0)
losses_std = data['losses'].std(0)
if args.captions:
caption = args.captions[i]
else:
caption = loss_fn
caption = '{} ({:.3f})'.format(caption, losses[-1])
plt.errorbar(iter, losses, yerr=losses_std, label=caption)
plt.legend()
plt.ylabel('Loss')
plt.xlabel('Iteration')
vz.savefig()
plt.close()
plt.figure()
for i, loss_fn in enumerate(args.losses):
print('file', loss_fn)
data = dd.io.load(loss_fn)
iter = data['iterations'][0]
rates = 100*(1-data['rates'].mean(0))
rates_std = 100*data['rates'].std(0)
if args.captions:
caption = args.captions[i]
else:
caption = loss_fn
caption = '{} ({:.2f}%)'.format(caption, rates[-1])
plt.errorbar(iter, rates, yerr=rates_std, label=caption)
plt.legend()
plt.ylabel('Error rate (%)')
plt.xlabel('Iteration')
vz.savefig()
plt.close()
def errorplot(x, y, minconf, maxconf, **kwargs):
'''
e.g.
g = sns.FacetGrid(attr, col='run', hue='subj_pos', col_wrap=5)
g = g.map(errorplot, 'n_diff_intervening', 'errorprob',
'minconf', 'maxconf').add_legend()
'''
plt.errorbar(x, y, yerr=[y - minconf, maxconf - y], fmt='o-', **kwargs)
def plot(x,y, error):
plt.plot(x, y,color='blue', linestyle='dashed')
plt.errorbar(x,y,yerr=error)
plt.title('Mean Number of Inflamation Bouts Per Day Of Trial')
plt.ylabel('Mean Number of Innflamation Bouts Reported Per Patient')
plt.xlabel('Days in Trial')
plt.grid(color='k', linestyle='--', linewidth=0.1)
plt.show()
def compareMasses(his, hiserr, mine, myerr, hisfield, hisid, myfield, myid, z):
import matplotlib.pylab as plt
a = []
b = []
c = []
d = []
e = []
for i in range(0, np.shape(mine)[0]):
if mine[i] != 0:
#his_id_idx = np.where(hisid == myid[i])[0]
pos_id_idx = np.where(hisid == myid[i])[0]
if len(pos_id_idx) == 1:
his_id_idx = int(pos_id_idx)
else:
pos_field_idx = np.where(hisfield == myfield[i])[0]
for ii in range(0, len(pos_field_idx)):
for iii in range(0, len(pos_id_idx)):
if pos_field_idx[ii] == pos_id_idx[iii]:
his_id_idx = int(pos_id_idx[iii])
#print str(myid[i]), str(myfield[i]), str(hisid[his_id_idx]), str(hisfield[his_id_idx])
assert myfield[i] == hisfield[his_id_idx]
assert myid[i] == hisid[his_id_idx]
if his[his_id_idx] != -999:
a.append(his[his_id_idx])
b.append(hiserr[his_id_idx])
c.append(mine[i]-np.log10(((1.0+z[i]))))#-np.log10(2.75))#(1.0+z[i]))
d.append(myerr[i,0]-np.log10(((1.0+z[i]))))#-np.log10(2.75))#1.0+z[i]))
e.append(myerr[i,1]-np.log10(1.0+z[i]))#-np.log10(2.75))#1.0+z[i]))
# since errors are just percentile, need difference from median
d = np.asarray(c)-np.asarray(d)
e = np.asarray(e)-np.asarray(c)
plt.errorbar(a, c, xerr=b, yerr=[d,e], fmt='o',
color='b', capsize=0, alpha=0.50)
# plot the y=x line
x = np.linspace(np.min((a,c)),
np.max((a,c)),
10)
plt.plot(x, x, 'k--')
'''
# plot the best fit line
m, b = np.polyfit(a, c, 1)
plt.plot(x, m*x + b, 'r--')
'''
plt.xlabel("Alex's log10(mass)")
plt.ylabel('MCSED log10(mass) / (1+z)')
plt.title("Alex's Masses vs MCSED Masses/(1+z)")#, Red=LineOfBestFit(m: "+str(m)+", b:"+str(b)+"), Black=OneToOneLine")
#plt.legend(['With Neb. Emis.'],loc=0)#, 'W/o Neb. Emis'], loc=0)
plt.show()
def plot_points(data, xpower=0):
"""Make a nice plot
"""
import matplotlib.pylab as plt
x = data[0]
y = data[1] * x ** xpower
ydn = data[2] * x ** xpower
yup = data[3] * x ** xpower
plt.errorbar(x, y, [ydn, yup], fmt='o', color='k')
def plot_barchart(values, main='', labels=None, errors=None):
"""Plot a bar chart and put labels (list) on the x-axis.
If 'errors' are given, show an error bar for each value.
"""
from matplotlib.pylab import errorbar
create_barchart(values, main=main, labels=labels)
if errors is not None:
errorbar(arange(values.size)+0.5, values, errors, fmt='o')
show_plots()
def plot_points(data, xpower=0):
"""Make a nice plot
"""
import matplotlib.pylab as plt
x = data[0]
y = data[1] * x**xpower
ydn = data[2] * x**xpower
yup = data[3] * x**xpower
plt.errorbar(x, y, [ydn, yup], fmt='o', color='k')
def plot_pop_size_across_time(params,
ymin=ymin,
ymax=ymax):
offset = step_size / 250.
x_offsets = [0, offset, 2*offset]
num_xticks = 11
ax = sns.tsplot(time="t", value="log2_pop_size", unit="sim_num",
condition="policy", color=policy_colors,
err_style=None,
data=df)
for policy_num, policy in enumerate(policy_colors):
error_df = summary_df[summary_df["policy"] == policy]
c = policy_colors[policy]
assert (len(error_df["t"]) == len(time_obj.t) == \
len(error_df["log2_pop_size"]["mean"]))
plt.errorbar(error_df["t"] + x_offsets[policy_num],
error_df["log2_pop_size"]["mean"],
yerr=error_df["log2_pop_size"]["std"].values,
color=c,
linestyle="none",
marker="o",
capsize=2,
capthick=1,
clip_on=False)
plt.xlabel(r"$t$")
plt.ylabel("Pop. size ($\log_{2}$)")
#
#\theta_{\mathsf{Gal}\rightarrow\mathsf{Glu}}
print "PARAMS: ", params
plt.title(r"$P_{0} = %d$, $\theta_{\mathsf{Glu}\rightarrow \mathsf{Glu}} = %.2f$, " \
r"$\theta_{\mathsf{Gal}\rightarrow \mathsf{Glu}} = %.2f$, " \
r"$\mu_{\mathsf{Glu}} = %.2f, \mu_{\mathsf{Gal}} = %.2f$, " \
r"$\mu_{\mathsf{Mis}} = %.2f$, lag = %d, " \
r"%d iters" %(sum(params["init_pop_size"]),
params["true_gluc_to_gluc"],
params["true_galac_to_gluc"],
params["gluc_growth_rate"],
params["galac_growth_rate"],
params["mismatch_growth_rate"],
params["decision_lag_time"],
params["num_sim_iters"]),
fontsize=8)
c = 0.5
plt.xlim([min(df["t"]) - c, max(df["t"]) + c])
if ymin is None:
ymin = int(np.log2(sum(params["init_pop_size"])))
if ymax is None:
ymax = int(error_df["log2_pop_size"]["mean"].max() + \
error_df["log2_pop_size"]["std"].max()) + 1
plt.ylim([ymin, ymax])
plt.xlim([time_obj.t.min(),
time_obj.t.max()])
# plt.yticks(range(ymin, ymax + 1))
plt.xticks(np.linspace(time_obj.t.min(),
time_obj.t.max(),
num_xticks))
sns.despine(trim=True, offset=time_obj.step_size*2)
def run_correlation_model(gp,
mp,
Xs,
Ys1,
Ys2,
Ys1err,
Ys2err,
mcmc_samples=500):
xbins = np.linspace(0.0, 2.0, 11)
xbins = [[xbins[i], xbins[i + 1]] for i in range(len(xbins) - 1)]
rmed = []
rmin = []
rmax = []
x = []
for xbin in (xbins):
mask = Xs.T[0] < xbin[1]
mask *= Xs.T[0] > xbin[0]
r, sig_1, sig_2 = estimate_property_covariance(
gp,
mp,
Xs[mask],
Ys1[mask],
Ys2[mask],
Ys1err[mask],
Ys2err[mask],
nu=4.0,
mcmc_samples=mcmc_samples)
rmed += [np.percentile(r, 50)]
rmin += [np.percentile(r, 50) - np.percentile(r, 16)]
rmax += [np.percentile(r, 84) - np.percentile(r, 50)]
x += [(xbin[1] + xbin[0]) / 2.0]
plt.errorbar(np.array(x),
np.array(x) * 0.0 + 0.5,
color='orange',
lw=5.0,
label='Input Correlation')
plt.errorbar(np.array(x),
rmed,
yerr=[rmin, rmax],
fmt='o',
label='Inferred')
plt.legend(loc=4, prop={'size': 18})
plt.xlabel('r', size=23)
plt.ylabel('correlation', size=23)
plt.ylim([-1, 1])
plt.grid()
check_directory('./plots/')
plt.savefig('./plots/inferred_correlations_fake_sim.png',
bbox_inches='tight')
def dynamo_spread(self,lethality_percent):
infected_percentage_points=51
iterations=200
results=list()
percent_dead_results = [[] for i in range(infected_percentage_points)]
percent_infected_results = [[] for i in range(infected_percentage_points)]
for iter in range(iterations):
dead = list()
infected = list()
num=random.randint(self.min,self.max)
if self.graph_type == "BA":
edges = self.gen_Barabasi_Albert(num, 4, 6)
else:
edges = self.gen_Watts_Strogatz(num, 10, 0.5)
for pre_infection_percent in range(infected_percentage_points):
percent=pre_infection_percent/float(infected_percentage_points-1)
verts = [0]*num
if self.infection_type=="degree":
verts = self.gen_infection_degreeranked(verts,edges,int(percent*num))
elif self.infection_type=="random":
verts = self.gen_infection_random(verts,edges,int(percent*num))
elif self.infection_type=="eigen":
verts = self.gen_infection_eigenranked(verts,edges,int(percent*num))
elif self.infection_type=="betweenness":
verts = self.gen_infection_betweennessranked(verts,edges,int(percent*num))
ftime,verts_out=self.spread(verts,edges,lethality_percent)
percent_dead = len([vertex for vertex in verts_out if vertex==3])/float(num)
percent_affect = len([vertex for vertex in verts_out if vertex!=0])/float(num)
percent_dead_results[pre_infection_percent].append(percent_dead)
percent_infected_results[pre_infection_percent].append(percent_affect)
#percent_dead_results = [percent_dead_results[m].append(dead[m]) for m in range(infected_percentage_points)]
#percent_infected_results = [percent_infected_results[m].append(infected[m]) for m in range(infected_percentage_points)]
#print percent_dead_results
#print percent_infected_results
if self.plot:
x = [location/float(infected_percentage_points-1) for location in range(0,infected_percentage_points)]
figure = plt.figure(1)
ax1 = figure.add_axes((.1,.4,.8,.5))
plt.clf()
yone = [mean(item) for item in percent_dead_results]
ytwo = [mean(item) for item in percent_infected_results]
print percent_infected_results
errorone = [2.58*std(item)/sqrt(len(item)) for item in percent_dead_results]
errortwo = [2.58*std(item)/sqrt(len(item)) for item in percent_infected_results]
print x
print ytwo, errortwo
one = pylab.errorbar(x,yone,yerr=errorone,fmt='ro')
two = pylab.errorbar(x,ytwo,yerr=errortwo,fmt='bo')
txt=", ".join(["Lethality of Infection: "+str(percent),"Averaged over "+str(iterations)+" distinct graphs\n","99% Confidence Interval","Min Graph Size: "+str(self.min),"Max Graph Size: "+str(self.max), "Infecting type: "+self.infection_type+"\n","Graph type: "+self.graph_type,"Mortality and Spread vs Infected Size"])
plt.title(txt,fontsize=10)
plt.legend([one,two],["Dead","Infected"])
plt.xlabel("Percent Infected")
plt.ylabel("Percent of Graph")
figure.savefig(", ".join([str(dt.now()),self.infection_type,self.graph_type])+"_dynamo_spread.png")
#plt.show()
return percent_dead_results, percent_infected_results
def plotData(date,loc,uncert,fil,dir):
os.chdir(dir)
fig = plt.figure()
plt.scatter(date,loc)
uncert = [u*3 for u in uncert]
plt.errorbar(date, loc, uncert, ls='none')
plt.savefig(fil + '.png')
plt.close(fig)
os.chdir('..')
return
def plotMultiStab(data_file, matrix_file):
data_dict = {}
stab_mat = np.load(matrix_file)
for line in open(data_file, "r"):
key, val = line.rstrip("\n").split("\t")
data_dict[key] = val
accord_err = np.std(stab_mat, axis=1)
accord_mean = np.mean(stab_mat, axis=1)
plt.errorbar(np.arange(len(stab_mat)), accord_mean, yerr=accord_err)
plt.show()
def clusterRTToverTime(rttEstimates, timeBin="60", outputDirectory="./rttDistributions/",
minEstimates=10, plot=True, logNormal=True):
"""For each IP address, find the different RTT distributions for each time
bin and plot the average value of each distribution.
"""
# for each IP in the traffic
ips = rttEstimates.index.unique()
for ip in ips:
start = rttEstimates[rttEstimates.index == ip].start_sec.min()
end = rttEstimates[rttEstimates.index == ip].start_sec.max()
dataIP = rttEstimates[rttEstimates.index == ip]
x = []
y = []
z = []
i = 0
for ts in range(start,end,timeBin):
if logNormal:
data = np.log10(dataIP[(dataIP.start_sec>=ts) & (dataIP.start_sec<ts+timeBin)].rtt)
else:
data = dataIP[(dataIP.start_sec>=ts) & (dataIP.start_sec<ts+timeBin)].rtt
# Look only at flows containing a certain number of RTT estimates
if len(data) < minEstimates:
sys.stderr("Ignoring data!! not enough samples!")
continue
# Cluster the data
vdp = dpgmm(data)
if vdp is None:
continue
params = NIWparam2Nparam(vdp)
if logNormal:
mean, std = logNormalMeanStdDev(params[0, :], params[1, :])
else:
mean = params[0, :]
std = params[1, :]
for mu, sig in zip(mean, std):
y.append(mu)
z.append(sig)
x.append(ts)
# Plot the clusters characteristics in a file
plt.figure()
plt.errorbar(x,y,yerr=z,fmt="o")
plt.grid(True)
if logNormal:
plt.savefig("{0}/{1}_timeBin{2}sec_logNormal.eps".format(outputDirectory, ip, timeBin))
else:
plt.savefig("{0}/{1}_timeBin{2}sec_normal.eps".format(outputDirectory, ip, timeBin))
def plot_hypothesis2():
with book_plots.figsize(y=2.5):
plt.figure()
plt.errorbar(range(1, 11), [169, 170, 169,171, 170, 171, 169, 170, 169, 170],
xerr=0, yerr=6, fmt='bo', capthick=2, capsize=10)
plt.plot([1, 10], [169, 170.5], color='g', ls='--')
plt.xlim(0, 11)
plt.ylim(150, 185)
plt.xlabel('day')
plt.ylabel('lbs')
def plot_table(table):
table1=np.array(table)
table1=table[table1[:,0].argsort()]
if len(table1.shape) != 2:
raise bad_table
if table1.shape[1]>=3:
plt.errorbar(table1[:,0],table1[:,1],yerr=table1[:,2],fmt='o')
else:
if table.shape[1]>=2:
plt.plot(table1[:,0],table1[:,1],marker='o')
else:
raise bad_table
def plot_vector(plt, title, na, label=''): #plt is the plot object #title is the plot title #na is the numpy array to be plotted avgIndex = 0 stdIndex = 1 y = na[:,avgIndex] err = na[:,stdIndex] plt.title(title) plt.errorbar(range(1,len(y)+1), y, yerr=err) plt.xlabel(label)
