def plot_p_leading_order(frame):
mat = scipy.io.loadmat('sound-speed_2D-wave.mat')
T=5; nt=T/0.5
pp=mat['U'][nt,:,:]
xx=mat['xx']
yy=mat['yy']
fig=pl.figure(figsize=(8, 3.5))
#pl.title("t= "+str(sol.state.t),fontsize=20)
pl.xticks(size=20); pl.yticks(size=20)
pl.xlabel('x',fontsize=20); pl.ylabel('y',fontsize=20)
#pl.pcolormesh(xx,yy,p_subxy,cmap=cm.OrRd)
pl.pcolormesh(xx,yy,pp,cmap='RdBu_r')
pl.autoscale(tight=True)
cb = pl.colorbar(ticks=[0.5,1,1.5,2]);
#pl.clim(ticks=[0.5,1,1.5,2])
imaxes = pl.gca(); pl.axes(cb.ax)
pl.yticks(fontsize=20); pl.axes(imaxes)
#pl.xticks(fontsize=20); pl.axes(imaxes)
#pl.axis('equal')
pl.axis('tight')
fig.tight_layout()
pl.savefig('./_plots_to_paper/sound-speed_LO_t'+str(frame)+'_pcolor.png')
pl.close()
def plot_field(self,x,y,u=None,v=None,F=None,contour=False,outdir=None,plot='quiver',figname='_field',format='eps'):
outdir = self.set_dir(outdir)
p = 64
if F is None: F=self.calc_F(u,v)
plt.close('all')
plt.figure()
#fig, axes = plt.subplots(nrows=1)
if contour:
plt.hold(True)
plt.contourf(x,y,F)
if plot=='quiver':
plt.quiver(x[::p],y[::p],u[::p],v[::p],scale=0.1)
if plot=='pcolor':
plt.pcolormesh(x[::4],y[::4],F[::4],cmap=plt.cm.Pastel1)
plt.colorbar()
if plot=='stream':
speed = F[::16]
plt.streamplot(x[::16], y[::16], u[::16], v[::16], density=(1,1),color='k')
plt.xlabel('$x$ (a.u.)')
plt.ylabel('$y$ (a.u.)')
plt.savefig(os.path.join(outdir,figname+'.'+format),format=format,dpi=320,bbox_inches='tight')
plt.close()
def showKernel(dataOrMatrix, fileName = None, useLabels = True, **args) :
labels = None
if hasattr(dataOrMatrix, 'type') and dataOrMatrix.type == 'dataset' :
data = dataOrMatrix
k = data.getKernelMatrix()
labels = data.labels
else :
k = dataOrMatrix
if 'labels' in args :
labels = args['labels']
import matplotlib
if fileName is not None and fileName.find('.eps') > 0 :
matplotlib.use('PS')
from matplotlib import pylab
pylab.matshow(k)
#pylab.show()
if useLabels and labels.L is not None :
numPatterns = 0
for i in range(labels.numClasses) :
numPatterns += labels.classSize[i]
#pylab.figtext(0.05, float(numPatterns) / len(labels), labels.classLabels[i])
#pylab.figtext(float(numPatterns) / len(labels), 0.05, labels.classLabels[i])
pylab.axhline(numPatterns, color = 'black', linewidth = 1)
pylab.axvline(numPatterns, color = 'black', linewidth = 1)
pylab.axis([0, len(labels), 0, len(labels)])
if fileName is not None :
pylab.savefig(fileName)
pylab.close()
def save(self, out_path):
'''Saves a figure for the monitor
Args:
out_path: str
'''
plt.clf()
np.set_printoptions(precision=4)
font = {
'size': 7
}
matplotlib.rc('font', **font)
y = 2
x = ((len(self.d) - 1) // y) + 1
fig, axes = plt.subplots(y, x)
fig.set_size_inches(20, 8)
for j, (k, v) in enumerate(self.d.iteritems()):
ax = axes[j // x, j % x]
ax.plot(v, label=k)
if k in self.d_valid.keys():
ax.plot(self.d_valid[k], label=k + '(valid)')
ax.set_title(k)
ax.legend()
plt.tight_layout()
plt.savefig(out_path, facecolor=(1, 1, 1))
plt.close()
def ploter(X,n,name,path,real_ranges = None):
'''
Graph plotting module. Very basic, so feel free to modify it.
'''
try: import matplotlib.pylab as plt
except ImportError:
print '\nMatplotlib is not installed! Either install it, or deselect graph option.\n'
return 1
lll = 1+len(X)/n
fig = plt.figure(figsize=(16,14),dpi=100)
for x in xrange(0,len(X),n):
iii = 1+x/n
ax = fig.add_subplot(lll,1,iii)
if real_ranges != None:
for p in real_ranges:
if p[0] in range(x,x+n) and p[1] in range(x,x+n): ax.axvspan(p[0]%(n), p[1]%(n), facecolor='g', alpha=0.5)
elif p[0] in range(x,x+n) and p[1] > x+n: ax.axvspan(p[0]%(n), n, facecolor='g', alpha=0.5)
elif p[0] < x and p[1] in range(x,x+n): ax.axvspan(0, p[1]%(n), facecolor='g', alpha=0.5)
elif p[0] < x and p[1] > x+n: ax.axvspan(0, n, facecolor='g', alpha=0.5)
ax.plot(X[x:x+n],'r-')
ax.set_xlim(0.,n)
ax.set_ylim(0.,1.)
ax.set_xticklabels(range(x,x+750,100)) #(x,x+n/5,x+2*n/5,x+3*n/5,x+4*n/5,x+5*n/5) )
plt.savefig(path+'HMM_'+name+'.png')
plt.close()
def plot_multi_format(plot_funcs, plot_kwargs=None,
usetex=False, outdir='plots',
setting_funcs=['single', 'span', 'slides', 'thumbnails']):
"""
Outputs plots formatted 4 ways: Publication ready (narrow and wide),
PowerPoint ready, and png thumbnails.
input
-----
plot_funcs : List of functions that return a mpl figure and a filename (or list of figures and filenames)
"""
setting_dict = {'single': mpl_single_column,
'span': mpl_span_columns,
'slides': mpl_slides,
'thumbnails': mpl_thumbnails}
if not os.path.exists(outdir):
os.makedirs(outdir)
# For python 3.4
# os.makedirs(outdir, exist_ok=True)
if plot_kwargs is None:
plot_kwargs=[{}]*len(plot_funcs)
for key in setting_funcs:
setting_dict[key](usetex=usetex)
for plot_func,pkwargs in zip(plot_funcs,plot_kwargs):
figs, names = plot_func(**pkwargs)
for fig,name in zip(figs,names):
fig.savefig(os.path.join(outdir, key+'_'+name))
plt.close('all')
def test_simple_gen(self):
self_con = .8
other_con = 0.05
g = self.gen.gen_stoch_blockmodel(min_degree=1, blocks=5, self_con=self_con, other_con=other_con,
powerlaw_exp=2.1, degree_seq='powerlaw', num_nodes=1000, num_links=3000)
deg_hist = vertex_hist(g, 'total')
res = fit_powerlaw.Fit(g.degree_property_map('total').a, discrete=True)
print 'powerlaw alpha:', res.power_law.alpha
print 'powerlaw xmin:', res.power_law.xmin
if len(deg_hist[0]) != len(deg_hist[1]):
deg_hist[1] = deg_hist[1][:len(deg_hist[0])]
print 'plot degree dist'
plt.plot(deg_hist[1], deg_hist[0])
plt.xscale('log')
plt.xlabel('degree')
plt.ylabel('#nodes')
plt.yscale('log')
plt.savefig('deg_dist_test.png')
plt.close('all')
print 'plot graph'
pos = sfdp_layout(g, groups=g.vp['com'], mu=3)
graph_draw(g, pos=pos, output='graph.png', output_size=(800, 800),
vertex_size=prop_to_size(g.degree_property_map('total'), mi=2, ma=30), vertex_color=[0., 0., 0., 1.],
vertex_fill_color=g.vp['com'],
bg_color=[1., 1., 1., 1.])
plt.close('all')
print 'init:', self_con / (self_con + other_con), other_con / (self_con + other_con)
print 'real:', gt_tools.get_graph_com_connectivity(g, 'com')
def plot_corner_posteriors(self, savefile=None, labels=["T1", "R1", "Av", "T2", "R2"]):
'''
Plots the corner plot of the MCMC results.
'''
ndim = len(self.sampler.flatchain[0,:])
chain = self.sampler
samples = chain.flatchain
samples = samples[:,0:ndim]
plt.figure(figsize=(8,8))
fig = corner.corner(samples, labels=labels[0:ndim])
plt.title("MJD: %.2f"%self.mjd)
name = self._get_save_path(savefile, "mcmc_posteriors")
plt.savefig(name)
plt.close("all")
plt.figure(figsize=(8,ndim*3))
for n in range(ndim):
plt.subplot(ndim,1,n+1)
chain = self.sampler.chain[:,:,n]
nwalk, nit = chain.shape
for i in np.arange(nwalk):
plt.plot(chain[i], lw=0.1)
plt.ylabel(labels[n])
plt.xlabel("Iteration")
name_walkers = self._get_save_path(savefile, "mcmc_walkers")
plt.tight_layout()
plt.savefig(name_walkers)
plt.close("all")
def viz_birth_proposal_2D(curModel, newModel, ktarget, freshCompIDs,
title1='Before Birth',
title2='After Birth'):
''' Create before/after visualization of a birth move (in 2D)
'''
from ..viz import GaussViz, BarsViz
from matplotlib import pylab
fig = pylab.figure()
h1 = pylab.subplot(1,2,1)
if curModel.obsModel.__class__.__name__.count('Gauss'):
GaussViz.plotGauss2DFromHModel(curModel, compsToHighlight=ktarget)
else:
BarsViz.plotBarsFromHModel(curModel, compsToHighlight=ktarget, figH=h1)
pylab.title(title1)
h2 = pylab.subplot(1,2,2)
if curModel.obsModel.__class__.__name__.count('Gauss'):
GaussViz.plotGauss2DFromHModel(newModel, compsToHighlight=freshCompIDs)
else:
BarsViz.plotBarsFromHModel(newModel, compsToHighlight=freshCompIDs, figH=h2)
pylab.title(title2)
pylab.show(block=False)
try:
x = raw_input('Press any key to continue >>')
except KeyboardInterrupt:
import sys
sys.exit(-1)
pylab.close()
def plot_size_of_c(size_of_c, path):
xlabel('|C|')
ylabel('Max model size |Ci|')
grid(True)
plot([x+1 for x in range(len(size_of_c))], size_of_c)
savefig(os.path.join(path, 'size_of_c.png'))
close()
def plot_q(frame,file_prefix='claw',file_format='petsc',path='./_output/',plot_pcolor=True,plot_slices=True,slices_xlimits=None):
import sys
sys.path.append('.')
import gaussian_1d
sol=Solution(frame,file_format=file_format,read_aux=False,path=path,file_prefix=file_prefix)
x=sol.state.grid.x.centers
mx=len(x)
bathymetry = 0.5
eta=sol.state.q[0,:] + bathymetry
if frame < 10:
str_frame = "00"+str(frame)
elif frame < 100:
str_frame = "0"+str(frame)
else:
str_frame = str(frame)
fig = pl.figure(figsize=(40,10))
ax = fig.add_subplot(111)
ax.set_aspect(aspect=1)
ax.plot(x,eta)
#pl.title("t= "+str(sol.state.t),fontsize=20)
#pl.xticks(size=20); pl.yticks(size=20)
#pl.xlim([0, gaussian_1d.Lx])
pl.ylim([0.5, 1.0])
pl.xlim([0., 4.0])
#pl.axis('equal')
pl.savefig('./_plots/eta_'+str_frame+'_slices.png')
pl.close()
def plot_heuristic(heuristic, path):
xlabel('|C|')
ylabel('h')
grid(True)
plot(heuristic)
savefig(os.path.join(path, 'heuristic.png'))
close()
def plot_running_time(running_time, path):
xlabel('|C|')
ylabel('MTV iteration in secs.')
grid(True)
plot([x for x in range(len(running_time))], running_time)
savefig(os.path.join(path, 'running_time.png'))
close()
def triple_plot(cccsum, cccsum_hist, trace, threshold, save=False,
savefile=''):
r"""Main function to make a triple plot with a day-long seismogram, \
day-long correlation sum trace and histogram of the correlation sum to \
show normality.
:type cccsum: numpy.ndarray
:param cccsum: Array of the cross-channel cross-correlation sum
:type cccsum_hist: numpy.ndarray
:param cccsum_hist: cccsum for histogram plotting, can be the same as \
cccsum but included if cccsum is just an envelope.
:type trace: obspy.Trace
:param trace: A sample trace from the same time as cccsum
:type threshold: float
:param threshold: Detection threshold within cccsum
:type save: bool, optional
:param save: If True will svae and not plot to screen, vice-versa if False
:type savefile: str, optional
:param savefile: Path to save figure to, only required if save=True
"""
if len(cccsum) != len(trace.data):
print('cccsum is: ' +
str(len(cccsum))+' trace is: '+str(len(trace.data)))
msg = ' '.join(['cccsum and trace must have the',
'same number of data points'])
raise ValueError(msg)
df = trace.stats.sampling_rate
npts = trace.stats.npts
t = np.arange(npts, dtype=np.float32) / (df * 3600)
# Generate the subplot for the seismic data
ax1 = plt.subplot2grid((2, 5), (0, 0), colspan=4)
ax1.plot(t, trace.data, 'k')
ax1.axis('tight')
ax1.set_ylim([-15 * np.mean(np.abs(trace.data)),
15 * np.mean(np.abs(trace.data))])
# Generate the subplot for the correlation sum data
ax2 = plt.subplot2grid((2, 5), (1, 0), colspan=4, sharex=ax1)
# Plot the threshold values
ax2.plot([min(t), max(t)], [threshold, threshold], color='r', lw=1,
label="Threshold")
ax2.plot([min(t), max(t)], [-threshold, -threshold], color='r', lw=1)
ax2.plot(t, cccsum, 'k')
ax2.axis('tight')
ax2.set_ylim([-1.7 * threshold, 1.7 * threshold])
ax2.set_xlabel("Time after %s [hr]" % trace.stats.starttime.isoformat())
# ax2.legend()
# Generate a small subplot for the histogram of the cccsum data
ax3 = plt.subplot2grid((2, 5), (1, 4), sharey=ax2)
ax3.hist(cccsum_hist, 200, normed=1, histtype='stepfilled',
orientation='horizontal', color='black')
ax3.set_ylim([-5, 5])
fig = plt.gcf()
fig.suptitle(trace.id)
fig.canvas.draw()
if not save:
plt.show()
plt.close()
else:
plt.savefig(savefile)
return
def plot_BIC_score(BIC_SCORE, path):
xlabel('|C|')
ylabel('BIC score')
grid(True)
plot(BIC_SCORE)
savefig(os.path.join(path, 'BIC.png'))
close()
def compareTwoUsers(data1, data2, outdir):
"""Compares data for two users. Currently plots difference in peaks for
the users on presslengths for different keycodes."""
def computePeakDifference(d1, d2):
edges = findCommonEdges(d1, d2)
h1, e = np.histogram(d1, bins=edges, normed=True)
h2, e = np.histogram(d2, bins=edges, normed=True)
a1, a2 = np.argmax(h1), np.argmax(h2)
diff = (edges[a1] + edges[a1 + 1] - edges[a2] - edges[a2 + 1]) / 2.0
return diff
commonKeys = set(data1.keystrokePLs_key.keys()) & set(data2.keystrokePLs_key.keys())
peakDiffs = []
for key in commonKeys:
dat1 = data1.keystrokePLs_key[key]
dat2 = data2.keystrokePLs_key[key]
peakDiffs.append(computePeakDifference(dat1, dat2))
peakDiffs.append(computePeakDifference(data1.keystrokePLs, data2.keystrokePLs))
edges = findCommonEdges(peakDiffs)
plt.figure()
plt.hist(peakDiffs, bins=edges)
plt.title("Peak Differences for Keystroke PL for %s and %s" % (data1.user, data2.user))
plt.xlabel("Time (seconds)")
plt.savefig("%s/%s_%s_kPLpeakDiff.pdf" % (outdir, data1.user, data2.user))
plt.close()
def threeD_gridplot(nodes, save=False, savefile=''):
r"""Function to plot in 3D a series of grid points.
:type nodes: list of tuples
:param nodes: List of tuples of the form (lat, long, depth)
:type save: bool
:param save: if True will save without plotting to screen, if False \
(default) will plot to screen but not save
:type savefile: str
:param savefile: required if save=True, path to save figure to.
"""
lats = []
longs = []
depths = []
for node in nodes:
lats.append(float(node[0]))
longs.append(float(node[1]))
depths.append(float(node[2]))
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(lats, longs, depths)
ax.set_ylabel("Latitude (deg)")
ax.set_xlabel("Longitude (deg)")
ax.set_zlabel("Depth(km)")
ax.get_xaxis().get_major_formatter().set_scientific(False)
ax.get_yaxis().get_major_formatter().set_scientific(False)
if not save:
plt.show()
plt.close()
else:
plt.savefig(savefile)
return
def plot_selfish_cooperative(num_runs):
import seaborn as sns
for exp in range(num_runs):
fig = plt.figure()
cooperators = [3,4,5]
selfish = [0,1,2]
fname = Parameters.dirname + '/%i_assembly_%i.dat' % (exp, 0)
t, pop = np.loadtxt(fname, unpack = True)
cooperative_pop = [0.0]*len(pop[:-5])
selfish_pop = [0.0]*len(pop[:-5])
for c in cooperators:
fname = Parameters.dirname + '/%i_assembly_%i.dat' % (exp, c)
t, pop = np.loadtxt(fname, unpack = True)
cooperative_pop = np.add(cooperative_pop,pop[:-5] )
for s in selfish:
fname = Parameters.dirname + '/%i_assembly_%i.dat' % (exp, s)
t, pop = np.loadtxt(fname, unpack = True)
selfish_pop = np.add(selfish_pop,pop[:-5] )
ax = fig.add_subplot(1,1,1)
ax.plot(t[:-5], selfish_pop, label = 'selfish', color = 'r')
ax.plot(t[:-5], cooperative_pop, label = 'cooperative', color = 'g')
ax.legend(loc = 'upper left')
plt.xlabel('System Time')
plt.ylabel('Total Abundance')
#plt.show()
plt.savefig(Parameters.dirname + '/%i_cooperative_vs_selfish.png' % exp)
plt.close()
def phase_space(self, resolution=200, initial_conds=[], fname_app=None):
"""
Plot phase space of system.
Arguments
resolution
Resolution of plot
initial_conds
List of initial conditions for trajectories
"""
fig = plt.figure()
self._plot_vector_field(resolution/10)
self._plot_nullclines(resolution)
self._plot_trajectories(initial_conds)
plt.xlabel(r'$\varphi_0$')
plt.ylabel(r'$\varphi_1$')
plt.title(
'Phase plane{}'.format(
'' if fname_app is None else ' ({})'.format(fname_app)))
plt.savefig(
'images/phase_space{}.pdf'.format(
'' if fname_app is None else '_{:04}'.format(fname_app)))
plt.close()
def plot(frame,dirname,clim=None,axis_limits=None):
if not os.path.exists('./figures'):
os.makedirs('./figures')
try:
sol=Solution(frame,file_format='petsc',read_aux=False,path='./saved_data/'+dirname+'/_p/',file_prefix='claw_p')
except IOError:
'Data file not found; please unzip the files in saved_data/.'
return
x=sol.state.grid.x.centers; y=sol.state.grid.y.centers
mx=len(x); my=len(y)
mp=sol.state.num_eqn
yy,xx = np.meshgrid(y,x)
p=sol.state.q[0,:,:]
if clim is not None:
pl.pcolormesh(xx,yy,p,cmap=cm.RdBu_r)
else:
pl.pcolormesh(xx,yy,p,cmap=cm.Reds)
pl.title("t= "+str(sol.state.t),fontsize=20)
pl.xticks(size=20); pl.yticks(size=20)
cb = pl.colorbar();
if clim is not None:
pl.clim(clim[0],clim[1]);
imaxes = pl.gca(); pl.axes(cb.ax)
pl.yticks(fontsize=20); pl.axes(imaxes)
pl.axis('equal')
if axis_limits is None:
pl.axis([np.min(x),np.max(x),np.min(y),np.max(y)])
else:
pl.axis([axis_limits[0],axis_limits[1],axis_limits[2],axis_limits[3]])
pl.savefig('./figures/'+dirname+'.png')
pl.close()
def _on_button_press(event):
if event.button != 1 or not event.inaxes:
return
lon, lat = m(event.xdata, event.ydata, inverse=True)
# Convert to colat to ease indexing.
colat = rotations.lat2colat(lat)
x_range = (self.setup["physical_boundaries_x"][1] -
self.setup["physical_boundaries_x"][0])
x_frac = (colat - self.setup["physical_boundaries_x"][0]) / x_range
x_index = int(((self.setup["boundaries_x"][1] -
self.setup["boundaries_x"][0]) * x_frac) +
self.setup["boundaries_x"][0])
y_range = (self.setup["physical_boundaries_y"][1] -
self.setup["physical_boundaries_y"][0])
y_frac = (lon - self.setup["physical_boundaries_y"][0]) / y_range
y_index = int(((self.setup["boundaries_y"][1] -
self.setup["boundaries_y"][0]) * y_frac) +
self.setup["boundaries_y"][0])
plt.figure(1, figsize=(3, 8))
depths = available_depths
values = data[x_index, y_index, :]
plt.plot(values, depths)
plt.grid()
plt.ylim(depths[-1], depths[0])
plt.show()
plt.close()
plt.figure(0)
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 plot_predlinks_roc(infile, outfile):
preddf = pickle.load(open(infile, 'r'))['df']
preddf['tp'] = preddf['t_t'] / preddf['t_tot']
preddf['fp'] = preddf['f_t'] / preddf['f_tot']
preddf['frac_wrong'] = 1.0 - (preddf['t_t'] + preddf['f_f']) / (preddf['t_tot'] + preddf['f_tot'])
f = pylab.figure(figsize=(2, 2))
ax = f.add_subplot(1, 1, 1)
# group by cv set
for row_name, cv_df in preddf.groupby('cv_idx'):
cv_df_m = cv_df.groupby('pred_thold').mean().sort('fp')
ax.plot(cv_df_m['fp'], cv_df_m['tp'] , c='k', alpha=0.3)
fname = infile[0].split('-')[0]
ax.set_title(fname)
ax.set_xticks([0.0, 1.0])
ax.set_yticks([0.0, 1.0])
ax.set_xlim(0, 1)
ax.set_ylim(0, 1)
f.savefig(outfile)
pylab.close(f)
def analyze(title, x, y, func, func_title):
print('-' * 80)
print(title)
print('x: %s:%s %s' % (list(x.shape), x.dtype, [x.min(), x.max()]))
print('y: %s:%s %s' % (list(y.shape), y.dtype, [y.min(), y.max()]))
popt, pcov = curve_fit(func, x, y)
print('popt=%s' % popt)
print('pcov=\n%s' % pcov)
a, b = popt
print('a=%e' % a)
print('b=%e' % b)
print(func_title(a, b))
xf = np.linspace(x.min(), x.max(), 100)
yf = func(xf, a, b)
print('xf: %s:%s %s' % (list(xf.shape), xf.dtype, [xf.min(), xf.max()]))
print('yf: %s:%s %s' % (list(yf.shape), yf.dtype, [yf.min(), yf.max()]))
plt.title(func_title(a, b))
# plt.xlim(0, x.max())
# plt.ylim(0, y.max())
plt.semilogx(x, y, label='data')
plt.semilogx(xf, yf, label='fit')
plt.legend(loc='best')
plt.savefig('%s.png' % title)
plt.close()
def check_HDF5(size=64):
"""
Plot images with landmarks to check the processing
"""
# Get hdf5 file
hdf5_file = os.path.join(data_dir, "CelebA_%s_data.h5" % size)
with h5py.File(hdf5_file, "r") as hf:
data_color = hf["training_color_data"]
data_lab = hf["training_lab_data"]
data_black = hf["training_black_data"]
for i in range(data_color.shape[0]):
fig = plt.figure()
gs = gridspec.GridSpec(3, 1)
for k in range(3):
ax = plt.subplot(gs[k])
if k == 0:
img = data_color[i, :, :, :].transpose(1,2,0)
ax.imshow(img)
elif k == 1:
img = data_lab[i, :, :, :].transpose(1,2,0)
img = color.lab2rgb(img)
ax.imshow(img)
elif k == 2:
img = data_black[i, 0, :, :] / 255.
ax.imshow(img, cmap="gray")
gs.tight_layout(fig)
plt.show()
plt.clf()
plt.close()
def test_PhysicalNodeLayout(self):
# # Graph: Physical Layout of Nodes
required_files = ["s1_layout." + img_extn]
#
for f in required_files:
try:
os.remove(f)
except:
pass
figsize = cb.latexify(columns=_texcol, factor=_texfac)
base_config = aietes.Simulation.populate_config(
aietes.Tools.get_config('bella_static.conf'),
retain_default=True
)
texify = lambda t: "${0}_{1}$".format(t[0], t[1])
node_positions = {texify(k): np.asarray(v['initial_position'], dtype=float) for k, v in
base_config['Node']['Nodes'].items() if 'initial_position' in v}
node_links = {0: [1, 2, 3], 1: [0, 1, 2, 3, 4, 5], 2: [0, 1, 5], 3: [0, 1, 4], 4: [1, 3, 5], 5: [1, 2, 4]}
fig = cb.plot_nodes(node_positions, figsize=figsize, node_links=node_links, radius=0, scalefree=True,
square=True)
fig.tight_layout(pad=0.3)
savefig(fig,"s1_layout", transparent=True)
plt.close(fig)
for f in required_files:
self.assertTrue(os.path.isfile(f))
self.generated_files.append(f)
def test_ThroughputLines(self):
# # Plot Throughput Lines
required_files = [
"throughput_sep_lines_static." + img_extn,
"throughput_sep_lines_all_mobile." + img_extn
]
for f in required_files:
try:
os.remove(f)
except:
pass
cb.latexify(columns=_texcol, factor=_texfac)
for mobility in mobilities:
df = get_mobility_stats(mobility)
fig = plt.figure(facecolor='white')
ax = fig.add_subplot(1, 1, 1)
for (k, g), ls in zip(df.groupby('separation'), itertools.cycle(["-", "--", "-.", ":"])):
ax.plot(g.rate, g.throughput, label=k, linestyle=ls)
ax.legend(loc="upper left")
ax.set_xlabel("Packet Emission Rate (pps)")
ax.set_ylabel("Avg. Throughput (bps)")
fig.tight_layout()
savefig(fig,"throughput_sep_lines_{0}".format(
mobility), transparent=True, facecolor='white')
plt.close(fig)
for f in required_files:
self.assertTrue(os.path.isfile(f))
self.generated_files.append(f)
def plot_df(self,show=False):
from matplotlib import pylab as plt
if self.afp is None:
print 'afp not initilized. call update afp'
return -1
linecords,td,df,rtn,minmaxy = self.afp
formatter = PlotDateFormatter(df.index)
#fig = plt.figure()
#ax = plt.addsubplot()
fig, ax = plt.subplots()
ax.xaxis.set_major_formatter(formatter)
ax.plot(np.arange(len(df)), df['p'])
for cord in linecords:
plt.plot(cord[0],cord[1],color='red')
fig.autofmt_xdate()
plt.xlim(-10,len(df.index) + 10)
plt.ylim(df.p.min() - 10,df.p.max() + 10)
plt.grid(ax)
#if show:
# plt.show()
#"{0}{1}.png".format("./data/",datetime.datetime.strftime(datetime.datetime.now(),'%Y%M%m%S'))
if self.plot_file:
save_path = self.plot_file.format(self.symbol)
if os.path.exists(os.path.dirname(save_path)):
plt.savefig(save_path)
plt.clf()
plt.close()
def plot_ea(frame1, filt_df, dst_path, uplift_rate, riv_case):
f = plt.figure()
ax = filt_df.plot(x='ApatiteHeAge', y='Elevation', style='o-', ax=f.gca())
plt.title('Age-Elevation')
plt.xlabel('ApatiteHeAge [Ma]')
plt.ylabel('Elevation [Km]')
#tread line
sup_age, slope, r_square = find_max_treadline(filt_df, uplift_rate * np.sin(np.deg2rad(60)), riv_case)
x = filt_df[filt_df['ApatiteHeAge'] < sup_age]['ApatiteHeAge']
y = filt_df[filt_df['ApatiteHeAge'] < sup_age]['Points:2']
z = np.polyfit(x, y, 1)
p = np.poly1d(z)
# plt.legend(point_lables, loc='best', fontsize=10)
# n = np.linspace(min(frame1[frame1['Points:2'] > min(frame1['Points:2'])]['ApatiteHeAge']), max(frame1['ApatiteHeAge']), 21)
n = np.linspace(min(filt_df[filt_df['Points:2'] >= min(filt_df['Points:2'])]['ApatiteHeAge']), max(filt_df['ApatiteHeAge']), 21)
plt.plot(n, p(n) - min(frame1['Points:2']),'-r')
ax.text(np.mean(n), np.mean(p(n) - min(frame1['Points:2'])), 'y=%.6fx + b'%(z[0]), fontsize = 20)
txs = np.linspace(np.round(min(filt_df['Elevation'])), np.ceil(max(filt_df['Elevation'])), 11)
lebs = ['0'] + [str(i) for i in txs[1:]]
plt.yticks(txs, list(reversed(lebs)))
plt.savefig(dst_path)
plt.close()
return z[0]
def test_one_box(box,tree,graphics=False,callback=None):#,f):
print 'box',box[0],box[1],':',
s = tree.search(box)
print ""
print "box search:", s
print "len(s):", len( s )
boxes = tree.boxes()
if graphics:
plt.close()
gfx.show_uboxes(boxes)
gfx.show_uboxes(boxes, S=s, col='r')
if len(s) < ((tree.dim**tree.depth)/2): # dim^depth/2
t = tree.insert(box)
if graphics:
boxes = tree.boxes()
gfx.show_uboxes(boxes, S=t, col='c')
print 'ins:',t
else:
t = tree.remove(s)
print 'rem:',t
if graphics:
gfx.show_box(box,col='g',alpha=0.5)
if callback:
plt.gcf().canvas.mpl_connect('button_press_event', callback)
plt.show()
def boxplot(pd_df,
features,
colsplitfeature,
cols,
celsplitfeature,
cels,
label={
'x': '',
'y': '',
'title': '',
'ticklabelssprecision': ''
},
order=None,
supress_plot=False,
figure_name='figure.png',
uselatex=False,
scalefont=1.):
"""This function plot a matrix of boxplot of correlations for several properties.
Parameters:
-----------
features: dict.
Mapping the features names (keys) and its label (values). The
order of the features in the figure follows the same order of the
presented in this dict.
colsplitfeature: str.
The scatternplot matrix will contain data splited per
column according to this feature values.
cols: dict.
Mapping the colsplitfeature feature values (keys) and its label (dict
values and column labels). The columns in the figure follows the same
order of this dict.
celsplitfeature: str or None.
The scatternplot matrix will contain data splited per
cell according to this feature values. None wil desable
multi plot per scattermatrix cell.
cels: dict or None.
If dict, it map the celsplitfeature feature value (keys) and its
labels (dict values and plot labels). The order of the plots in the
cells in the figure follows the same order of this dict.
labels: a dict ({'x': '', 'y': '', 'title': '', ticklabelssprecision=''})
The x, y, and the title labels.
figure_name: str, (figure.png).
The name of the figure.
uselatex: bollean, (False)
If True, the figure text will copiled with latex.
scalefont: float, (1.)
Scale the fontsize by this factor.
Return:
-------
XXX
A dictionary with the folloyings keys:
'corrs': np.array of floats with three dimentions.
The correlations calculated with cbcomp function.
If the plot were calculated:
'fig': pyplot figure.
The figure.
'axis': pyplat axis.
The axis.
'angular_parameter': np.array of floats with three dimentions.
The angular parameters of the linear model
fitting the data.
If bootstrap were employed:
'alt_test', 'null_test': np.array of booleans with three dimentions.
The result of the hypothesis test, H1 and
H0, respectively.
'null_test_pval': np.array of floats with three dimentions.
The p-values.
'alt_test_confimax', 'alt_test_confimin': np.array of booleans with
three dimentions.
Confidence maximum and
minimun.
"""
print("Initializing scatter plot")
# If were requested, latex will be employed to build the figure.
#if uselatex:
rc('text', usetex=True)
rcParams['text.latex.preamble'] = [
r'\usepackage[version=4]{mhchem} \usepackage{amsmath}'
r'\usepackage{amsfonts} \usepackage{mathtools}'
r'\usepackage[T1]{fontenc} \boldmath'
]
rcParams['axes.titleweight'] = 'bold'
# Features:
if not isinstance(features, dict):
print("Error: features should be a dictionary!")
sys.exit(1)
checkmissingkeys(
list(features.keys()), pd_df.columns.to_list(), "the "
"pandas.DataFrame does not present the following "
"features")
# Cells:
# if there only one plot per cell, a fake dimension will be crated
if celsplitfeature is None:
celsplitfeature = 'fake_celsplitfeature'
pd_df[celsplitfeature] = np.ones(len(pd_df))
cels = {1: ''}
if colsplitfeature is None:
colsplitfeature = 'fake_colsplitfeature'
pd_df[colsplitfeature] = np.ones(len(pd_df))
cols = {1: ''}
grouped = pd_df.groupby([colsplitfeature, celsplitfeature])
depth = len(cels)
height = len(features)
width = len(cols)
print('depth:', depth, 'height:', height, 'width:', width)
# creating empth plot!
plt.close('all')
figwidth = int((width * 1.) * 2)
figheight = int((height * 1.) * 2)
fig, axis = plt.subplots(nrows=height,
ncols=width,
sharex='col',
sharey='row',
figsize=(figwidth, figheight))
# label sizes:
axis_title_font_size = 30 * scalefont
axis_label_font_size = 25 * scalefont
tick_label_font_size = 25 * scalefont
anotation_font_size = 20
marker_size = 50
# Symbols/markers, lines,
slines = ['-', '--', ':', '-.']
scolors = ['y', 'g', 'm', 'c', 'b', 'r']
smarker = ['o', 's', 'D', '^', '*', 'o', 's', 'x', 'D', '+', '^', 'v', '>']
# Adding the scatterplos and linear models
size = len(pd_df)
nouts = np.zeros((height, width, depth))
ndata = np.zeros((height, width, depth))
#print(nouts)
for indf, feature in enumerate(list(features.keys())):
for colindex, colvals in enumerate(list(cols.keys())):
if len(cels) > 1:
# plot
boxplot = sns.boxplot(
x=celsplitfeature,
y=feature,
data=pd_df[pd_df[colsplitfeature] == colvals],
orient='v',
order=order,
ax=axis[indf, colindex])
# info
for celindex, celvals in enumerate(list(cels.keys())):
aux = np.logical_and(
np.array(pd_df[colsplitfeature].to_numpy()) == colvals,
np.array(pd_df[celsplitfeature].to_numpy()) == celvals)
aux2 = pd_df[aux]
data = np.array(aux2[feature].to_numpy())
output = boxplot_info(data)
ndata[indf, colindex, celindex] = output[-2]
nouts[indf, colindex, celindex] = output[-1]
else:
# plot
boxplot = sns.boxplot(
x=feature,
data=pd_df[pd_df[colsplitfeature] == colvals],
orient='v',
order=order,
ax=axis[indf, colindex])
# info
data = np.array(pd_df[pd_df[colsplitfeature] == colvals]
[feature].to_numpy())
output = boxplot_info(data)
ndata[indf, colindex, 0] = output[-2]
nouts[indf, colindex, 0] = output[-1]
# removind individual plots labels
boxplot.set_xlabel('')
boxplot.set_ylabel('')
#print
# per feature
for indf, feature in enumerate(list(features.keys())):
print("{}: {:.3f}%".format(
features[feature],
100 * np.sum(nouts[indf, :, :]) / np.sum(ndata[indf, :, :])))
# per column
for colindex, colvals in enumerate(list(cols.keys())):
print("{}: {:.3f}%".format(
cols[colvals], 100 * np.sum(nouts[:, colindex, :]) /
np.sum(ndata[:, colindex, :])))
# per cell
if len(cels) > 1:
for celindex, celvals in enumerate(list(cels.keys())):
print("{}: {:.3f}%".format(
cels[celvals], 100 * np.sum(nouts[:, :, celindex]) /
np.sum(ndata[:, :, celindex])))
# total
print('Total: {:.3f}%'.format(100 * np.sum(nouts) / np.sum(ndata)))
# adding labels
for indf, feature in enumerate(list(features.keys())):
for colindex, colvals in enumerate(list(cols.keys())):
if True:
axis[indf, colindex].xaxis.set_tick_params(direction='in',
length=5,
width=0.9)
axis[indf, colindex].yaxis.set_tick_params(direction='in',
length=5,
width=0.9)
# Ajuste do alinhamento dos labels, quantidade de casa deciamais,
axis[0, colindex].xaxis.set_label_position("top")
axis[0, colindex].set_xlabel(cols[colvals],
va='center',
ha='center',
labelpad=40,
size=axis_label_font_size)
axis[indf, 0].set_ylabel(features[feature],
va='center',
ha='center',
labelpad=40,
size=axis_label_font_size,
rotation=60)
for tikslabel in axis[indf, 0].yaxis.get_ticklabels():
tikslabel.set_fontsize(tick_label_font_size)
for tikslabel in axis[-1, colindex].xaxis.get_ticklabels():
tikslabel.set_fontsize(tick_label_font_size)
#tikslabel.set_rotation(60)
#y = label['ticklabelssprecision'][1][indf]
#x = label['ticklabelssprecision'][0]
#print(list(axis[indf, colindex].xaxis.get_ticklabels()))
#axis[indf, colindex].xaxis.set_major_formatter(FormatStrFormatter('%0.'+str(x)+'f'))
#axis[indf, colindex].yaxis.set_major_formatter(FormatStrFormatter('%0.'+str(y)+'f'))
#print(list(axis[indf, colindex].xaxis.get_ticklabels()))
#axis[indf, colindex].xaxis.set_major_locator(plt.MaxNLocator(3))
#axis[indf, colindex].yaxis.set_major_locator(plt.MaxNLocator(3))
#axis[indf, colindex].xaxis.set_ticklabels(axis[indf, colindex].xaxis.get_ticklabels(), {'fontweight':'bold'})
#axis[indf, colindex].yaxis.set_ticklabels(axis[indf, colindex].yaxis.get_ticklabels(), {'fontweight':'bold'})
#axis[indf, colindex].xaxis.set_major_formatter(width='bold')
#axis[indf, colindex].yaxis.set_major_formatter(width='bold')
plt.subplots_adjust(left=0.125,
right=0.92,
bottom=0.1,
top=0.9,
wspace=0.0,
hspace=0.0)
# Adicionando os principais captions da figura.
fig.text(0.01,
0.524,
label['y'],
ha='center',
rotation='vertical',
size=axis_title_font_size)
fig.text(0.5, 0.95, label['title'], ha='center', size=axis_title_font_size)
fig.text(0.5, 0.01, label['x'], ha='center', size=axis_title_font_size)
# Salvando a figura para um arquivo
plt.savefig(figure_name, dpi=300)
return
plt.savefig(
"diagrams/TKR4p149/pathways/pathways_zm_del_{0}.png".format(base),
dpi=400,
bbox_inches='tight')
dann.remove()
lann = plt.text(simX(0.345, 0.3), simY(0.3), r'L', fontsize=14)
plt.xlim([0.45, 0.55])
plt.ylim([0.25, 0.25 + rt3by2 * 0.1])
plt.savefig(
"diagrams/TKR4p149/pathways/pathways_zm_lav_{0}.png".format(base),
dpi=400,
bbox_inches='tight')
plt.close()
# Plot phase diagram
plt.figure(1, figsize=(10, 7.5)) # inches
plt.plot(XS, YS, '-k')
plt.plot(X0, Y0, '-k', zorder=1)
plt.axis('off')
gann = plt.text(simX(0.010, 0.495),
simY(0.495),
r'$\gamma$',
fontsize=14)
dann = plt.text(simX(0.230, 0.010),
simY(0.010),
r'$\delta$',
fontsize=14)
lann = plt.text(simX(0.340, 0.275), simY(0.275), r'L', fontsize=14)
def triple_plot(cccsum,
cccsum_hist,
trace,
threshold,
save=False,
savefile=''):
r"""Main function to make a triple plot with a day-long seismogram, \
day-long correlation sum trace and histogram of the correlation sum to \
show normality.
:type cccsum: numpy.ndarray
:param cccsum: Array of the cross-channel cross-correlation sum
:type cccsum_hist: numpy.ndarray
:param cccsum_hist: cccsum for histogram plotting, can be the same as \
cccsum but included if cccsum is just an envelope.
:type trace: obspy.Trace
:param trace: A sample trace from the same time as cccsum
:type threshold: float
:param threshold: Detection threshold within cccsum
:type save: bool, optional
:param save: If True will svae and not plot to screen, vice-versa if False
:type savefile: str, optional
:param savefile: Path to save figure to, only required if save=True
"""
if len(cccsum) != len(trace.data):
print('cccsum is: ' + str(len(cccsum)) + ' trace is: ' +
str(len(trace.data)))
msg = ' '.join(
['cccsum and trace must have the', 'same number of data points'])
raise ValueError(msg)
df = trace.stats.sampling_rate
npts = trace.stats.npts
t = np.arange(npts, dtype=np.float32) / (df * 3600)
# Generate the subplot for the seismic data
ax1 = plt.subplot2grid((2, 5), (0, 0), colspan=4)
ax1.plot(t, trace.data, 'k')
ax1.axis('tight')
ax1.set_ylim(
[-15 * np.mean(np.abs(trace.data)), 15 * np.mean(np.abs(trace.data))])
# Generate the subplot for the correlation sum data
ax2 = plt.subplot2grid((2, 5), (1, 0), colspan=4, sharex=ax1)
# Plot the threshold values
ax2.plot([min(t), max(t)], [threshold, threshold],
color='r',
lw=1,
label="Threshold")
ax2.plot([min(t), max(t)], [-threshold, -threshold], color='r', lw=1)
ax2.plot(t, cccsum, 'k')
ax2.axis('tight')
ax2.set_ylim([-1.7 * threshold, 1.7 * threshold])
ax2.set_xlabel("Time after %s [hr]" % trace.stats.starttime.isoformat())
# ax2.legend()
# Generate a small subplot for the histogram of the cccsum data
ax3 = plt.subplot2grid((2, 5), (1, 4), sharey=ax2)
ax3.hist(cccsum_hist,
200,
normed=1,
histtype='stepfilled',
orientation='horizontal',
color='black')
ax3.set_ylim([-5, 5])
fig = plt.gcf()
fig.suptitle(trace.id)
fig.canvas.draw()
if not save:
plt.show()
plt.close()
else:
plt.savefig(savefile)
return
def NR_plot(stream,
NR_stream,
detections,
false_detections=False,
size=(18.5, 10),
save=False,
title=False):
r"""Function to plot the Network response alongside the streams used -\
highlights detection times in the network response.
:type stream: :class: obspy.Stream
:param stream: Stream to plot
:type NR_stream: :class: obspy.Stream
:param NR_stream: Stream for the network response
:type detections: list of datetime objects
:param detections: List of the detections
:type false_detections: list of datetime
:param false_detections: Either False (default) or list of false detection\
times
:type size: tuple
:param size: Size of figure, default is (18.5,10)
:type save: bool
:param save: Save figure or plot to screen, if not False, must be string\
of save path.
:type title: str
:param title: String for the title of the plot, set to False
"""
import datetime as dt
import matplotlib.dates as mdates
fig, axes = plt.subplots(len(stream) + 1, 1, sharex=True, figsize=size)
if len(stream) > 1:
axes = axes.ravel()
else:
return
mintime = stream.sort(['starttime'])[0].stats.starttime
stream.sort(['network', 'station', 'starttime'])
for i, tr in enumerate(stream):
delay = tr.stats.starttime - mintime
delay *= tr.stats.sampling_rate
y = tr.data
x = [
tr.stats.starttime +
dt.timedelta(seconds=s / tr.stats.sampling_rate)
for s in xrange(len(y))
]
x = mdates.date2num(x)
axes[i].plot(x, y, 'k', linewidth=1.1)
axes[i].set_ylabel(tr.stats.station + '.' + tr.stats.channel,
rotation=0)
axes[i].yaxis.set_ticks([])
axes[i].set_xlim(x[0], x[-1])
# Plot the network response
tr = NR_stream[0]
delay = tr.stats.starttime - mintime
delay *= tr.stats.sampling_rate
y = tr.data
x = [
tr.stats.starttime + dt.timedelta(seconds=s / tr.stats.sampling_rate)
for s in range(len(y))
]
x = mdates.date2num(x)
axes[i].plot(x, y, 'k', linewidth=1.1)
axes[i].set_ylabel(tr.stats.station + '.' + tr.stats.channel, rotation=0)
axes[i].yaxis.set_ticks([])
axes[-1].set_xlabel('Time')
axes[-1].set_xlim(x[0], x[-1])
# Plot the detections!
ymin, ymax = axes[-1].get_ylim()
if false_detections:
for detection in false_detections:
xd = mdates.date2num(detection)
axes[-1].plot((xd, xd), (ymin, ymax),
'k--',
linewidth=0.5,
alpha=0.5)
for detection in detections:
xd = mdates.date2num(detection)
axes[-1].plot((xd, xd), (ymin, ymax), 'r--', linewidth=0.75)
# Set formatters for x-labels
mins = mdates.MinuteLocator()
timedif = tr.stats.endtime.datetime - tr.stats.starttime.datetime
if timedif.total_seconds() >= 10800 and timedif.total_seconds() <= 25200:
hours = mdates.MinuteLocator(byminute=[0, 15, 30, 45])
elif timedif.total_seconds() <= 1200:
hours = mdates.MinuteLocator(byminute=range(0, 60, 2))
elif timedif.total_seconds > 25200 and timedif.total_seconds() <= 172800:
hours = mdates.HourLocator(byhour=range(0, 24, 3))
elif timedif.total_seconds() > 172800:
hours = mdates.DayLocator()
else:
hours = mdates.MinuteLocator(byminute=range(0, 60, 5))
hrFMT = mdates.DateFormatter('%Y/%m/%d %H:%M:%S')
axes[-1].xaxis.set_major_locator(hours)
axes[-1].xaxis.set_major_formatter(hrFMT)
axes[-1].xaxis.set_minor_locator(mins)
plt.gcf().autofmt_xdate()
axes[-1].fmt_xdata = mdates.DateFormatter('%Y/%m/%d %H:%M:%S')
plt.subplots_adjust(hspace=0)
if title:
axes[0].set_title(title)
if not save:
plt.show()
plt.close()
else:
plt.savefig(save)
return
def pretty_template_plot(template,
size=(18.5, 10.5),
save=False,
title=False,
background=False,
picks=False):
r"""Function to make a pretty plot of a single template, designed to work \
better than the default obspy plotting routine for short data lengths.
:type template: :class: obspy.Stream
:param template: Template stream to plot
:type size: tuple
:param size: tuple of plot size
:type save: bool
:param save: if False will plot to screen, if True will save
:type title: bool
:param title: String if set will be the plot title
:type background: :class: obspy.stream
:param background: Stream to plot the template within.
:type picks: list of :class: eqcorrscan.utils.Sfile_util.PICK
:param picks: List of eqcorrscan type picks.
"""
fig, axes = plt.subplots(len(template), 1, sharex=True, figsize=size)
if len(template) > 1:
axes = axes.ravel()
else:
return
if not background:
mintime = template.sort(['starttime'])[0].stats.starttime
else:
mintime = background.sort(['starttime'])[0].stats.starttime
template.sort(['network', 'station', 'starttime'])
lengths = []
for i, tr in enumerate(template):
delay = tr.stats.starttime - mintime
y = tr.data
x = np.linspace(0, len(y) * tr.stats.delta, len(y))
x += delay
if background:
btr = background.select(station=tr.stats.station,
channel=tr.stats.channel)[0]
bdelay = btr.stats.starttime - mintime
by = btr.data
bx = np.linspace(0, len(by) * btr.stats.delta, len(by))
bx += bdelay
axes[i].plot(bx, by, 'k', linewidth=1)
axes[i].plot(x, y, 'r', linewidth=1.1)
lengths.append(max(bx[-1], x[-1]))
else:
axes[i].plot(x, y, 'k', linewidth=1.1)
lengths.append(x[-1])
# print(' '.join([tr.stats.station, str(len(x)), str(len(y))]))
axes[i].set_ylabel('.'.join([tr.stats.station, tr.stats.channel]),
rotation=0,
horizontalalignment='right')
axes[i].yaxis.set_ticks([])
# Plot the picks if they are given
if picks:
tr_picks = [
pick for pick in picks
if pick.station == tr.stats.station and pick.channel[0] +
pick.channel[-1] == tr.stats.channel[0] + tr.stats.channel[-1]
]
for pick in tr_picks:
if pick.phase == 'P':
pcolor = 'red'
elif pick.phase == 'S':
pcolor = 'blue'
else:
pcolor = 'k'
pdelay = pick.time - mintime
# print(pdelay)
axes[i].axvline(x=pdelay, color=pcolor, linewidth=2)
# axes[i].plot([pdelay, pdelay], [])
axes[i].set_xlim([0, max(lengths)])
axes[len(template) - 1].set_xlabel('Time (s) from start of template')
plt.subplots_adjust(hspace=0, left=0.175, right=0.95, bottom=0.07)
if title:
axes[0].set_title(title)
else:
plt.subplots_adjust(top=0.98)
if not save:
plt.show()
plt.close()
else:
plt.savefig(save)
def quit(self):
''' Have to explicitly call quit, in order to close all of the plot windows.
'''
close('all')
exit()
"""
import numpy as np
from numpy import pi as pi
import matplotlib.pylab as plt
from time import clock
from CREATE_IDEAL_MESH import *
from Meshing_Tools import *
from VISUAL_TRI import *
from IC_conditions import *
from HLLC_FLUX import *
from HLLC_SOLVER_TRI import *
plt.close('all')
# -----------------------------------------------------------
# case 3: INITIAL CONDITIONS IN EACH QUADRANT
# (p,d,u,v)
# -----------------------------------------------------------
upper_left = [0.3, 0.5323, 1.206, 0.0]
lower_left = [0.029, 0.138, 1.206, 1.206]
upper_right = [1.5, 1.5, 0.0, 0.0]
lower_right = [0.3, 0.5323, 0.0, 1.206]
# simulation time and Courant number for stability
sim_time = 0.3 # simulation time
CFL = 0.1 # Courant number
# -----------------------------------------------------------
def scatter_colorbar(pd_df,
mainprop,
features,
colsplitfeature,
cols,
celsplitfeature,
cels,
show='',
label={
'x': '',
'y': '',
'title': '',
'ticklabelssprecision': ''
},
cbcomp=comp_spearman,
cb_info={
'min': -1.,
'max': 1.,
'label': ''
},
bootstrap_info={
'n': 0,
'alpha': 0.25
},
supress_plot=False,
figure_name='figure.png',
uselatex=False,
scalefont=1.):
"""This function plot a scatterplot of correlations between properties and
a target property.
Parameters:
-----------
mainprop: str.
This feature will be the horizontal cell axes, shered
whichin each column.
features: dict.
Mapping the features names (keys) and its label (values). The
order of the features in the figure follows the same order of the
presented in this dict.
colsplitfeature: str.
The scatternplot matrix will contain data splited per
column according to this feature values.
cols: dict.
Mapping the colsplitfeature feature values (keys) and its label (dict
values and column labels). The columns in the figure follows the same
order of this dict.
celsplitfeature: str or None.
The scatternplot matrix will contain data splited per
cell according to this feature values. None wil desable
multi plot per scattermatrix cell.
cels: dict or None.
If dict, it map the celsplitfeature feature value (keys) and its
labels (dict values and plot labels). The order of the plots in the
cells in the figure follows the same order of this dict.
labels: a dict ({'x': '', 'y': '', 'title': '', ticklabelssprecision=''})
The x, y, and the title labels.
cbcomp: function,
function that compute the information (correlation/mutual info)
with the paired data.
cb_info: dict with three values ({'min'=-1.,'max'=1.,'label'=''}).
The max and min values for the colorbar values and its label.
bootstrap_info: a dict with three ({n=0,alpha=0.25,show:test,corrcut=0}).
If 'n' value were larger then zero the bootstrap analysis
will be performed with (under the null and alternative
hypothesis) with number of bootstraped samples equal to 'n'
value and a conconfidence level 'alpha'.
Moreover, the it will make return pvalues and both
hypothese test results.
show: str ['corr','pval', 'test', 'testred', 'ang', 'confint'].
Define what information will be shown in the scatterplot, if
bootstrap were employed.
If 'corr', the correlation value will be printed.
If 'test', the information whether the correlation pass in the
bootstrap hypothesis tests or not will be presented.
If 'testred', the following information will be printed: * if the
correlation passed in both tests, + if the correlaiton passed in
one test, and nothing if the correlation fail for both tests.
If 'pval', the p-value of the correlation bootstrap under null
hypothesis test will be shown.
If 'confint', the confidence interval for the correlations will be
show.
If 'ang', the angular value of the linear regression will be show.
If '', nothing will be show.
figure_name: str, (figure.png).
The name of the figure.
uselatex: bollean, (False)
If True, the figure text will copiled with latex.
scalefont: float, (1.)
Scale the fontsize by this factor.
Return:
-------
A dictionary with the folloyings keys:
'corrs': np.array of floats with three dimentions.
The correlations calculated with cbcomp function.
If the plot were calculated:
'fig': pyplot figure.
The figure.
'axis': pyplat axis.
The axis.
'angular_parameter': np.array of floats with three dimentions.
The angular parameters of the linear model
fitting the data.
If bootstrap were employed:
'alt_test', 'null_test': np.array of booleans with three dimentions.
The result of the hypothesis test, H1 and
H0, respectively.
'null_test_pval': np.array of floats with three dimentions.
The p-values.
'alt_test_confimax', 'alt_test_confimin': np.array of booleans with
three dimentions.
Confidence maximum and
minimun.
"""
print("Initializing scatter plot")
# If were requested, latex will be employed to build the figure.
if uselatex:
rc('text', usetex=True)
rcParams[
'text.latex.preamble'] = r'\usepackage[version=4]{mhchem} \usepackage{amsmath} \usepackage{amsfonts} \usepackage{mathtools} \usepackage[T1]{fontenc}' # \boldmath'
#rcParams['axes.titleweight'] = 'bold'
# Features:
if not isinstance(features, dict):
print("Error: features should be a dictionary!")
sys.exit(1)
checkmissingkeys(
list(features.keys()), pd_df.columns.to_list(), "the "
"pandas.DataFrame does not present the following "
"features")
# Cells:
# if there only one plot per cell, a fake dimension will be crated
if celsplitfeature is None:
celsplitfeature = 'fake_celsplitfeature'
pd_df[celsplitfeature] = np.ones(len(pd_df))
cels = {1: ''}
if colsplitfeature is None:
colsplitfeature = 'fake_colsplitfeature'
pd_df[colsplitfeature] = np.ones(len(pd_df))
cols = {1: ''}
grouped = pd_df.groupby([colsplitfeature, celsplitfeature])
depth = len(cels)
height = len(features)
width = len(cols)
print('depth:', depth, 'height:', height, 'width:', width)
# Calcalationg the property to be ploted in colors
corrs_plot = np.zeros([depth, height, width])
test_apply = np.zeros([depth, height, width], dtype=bool)
for findex, feature in enumerate(list(features.keys())):
for colindex, colvals in enumerate(list(cols.keys())):
for celindex, celvals in enumerate(list(cels.keys())):
try:
group = grouped.get_group((colvals, celvals))
except KeyError:
continue
datax, datay = tonparray(group[mainprop], group[feature])
if (len(datax) > 1) and (not np.all(datax == datax[0])) and (
not np.all(datay == datay[0])):
test_apply[celindex, findex, colindex] = True
corrs_plot[celindex, findex,
colindex] = cbcomp(datax, datay)
else:
corrs_plot[celindex, findex, colindex] = 0
corrs_plot = np.nan_to_num(corrs_plot)
# Correlation Bootstrap
if bootstrap_info['n']: # bootstraping the correlations
print('Bootstrap analysis')
null_test = np.zeros([depth, height, width], dtype=bool)
null_test_pval = np.zeros([depth, height, width], dtype=float)
alt_test = np.zeros([depth, height, width], dtype=bool)
alt_test_confimax = np.zeros([depth, height, width], dtype=float)
alt_test_confimin = np.zeros([depth, height, width], dtype=float)
for findex, feature in enumerate(list(features.keys())):
for colindex, colvals in enumerate(list(cols.keys())):
for celindex, celvals in enumerate(list(cels.keys())):
group = grouped.get_group((colvals, celvals))
datax, datay = tonparray(group[mainprop], group[feature])
if test_apply[celindex, findex, colindex]:
# null hypothesisi
test, pval = bstnull(datay,
datax,
corr_method=cbcomp,
nresamp=bootstrap_info['n'],
alpha=bootstrap_info['alpha'])
null_test[celindex, findex, colindex] = test
null_test_pval[celindex, findex, colindex] = pval
# alternative hypothesis
test, confi = bstalt(datay,
datax,
corr_method=cbcomp,
nresamp=bootstrap_info['n'],
alpha=bootstrap_info['alpha'])
alt_test[celindex, findex, colindex] = test
alt_test_confimax[celindex, findex,
colindex] = confi[1]
alt_test_confimin[celindex, findex,
colindex] = confi[0]
print("completed: ", findex + 1, ' of ', len(features))
# printing latex table
if False: #TODO correct this if statement
np.set_printoptions(formatter={'float': '{: 0.2f}'.format})
s = ' & '
sup = np.array(np.round(alt_test_confimax, 2), str)
inf = np.array(np.round(alt_test_confimin, 2), str)
r = np.vectorize(lambda t1, t2: t1 + ',' + t2)(sup, inf)
if r.shape[0] > 1:
firstrow = s + s
for colindex, colvals in enumerate(list(cols.keys())):
firstrow += cols[colvals] + s
firstrow += ' \\\\'
print(firstrow)
for indf, feature in enumerate(list(features.keys())):
for celindex, celvals in enumerate(list(cels.keys())):
rowtotalsup = features[feature] + s
rowtotalinf = s
rowtotalsup += cels[celvals] + s + 'sup' + s
rowtotalinf += s + 'inf' + s
for colindex, colvals in enumerate(list(cols.keys())):
rowtotalsup += sup[celindex, indf, colindex] + s
rowtotalinf += inf[celindex, indf, colindex] + s
print(rowtotalsup + ' \\\\')
print(rowtotalinf + ' \\\\')
else:
firstrow = s
for colindex, colvals in enumerate(list(cols.keys())):
firstrow += cols[colvals] + s + s
firstrow += ' \\\\'
print(firstrow)
for indf, feature in enumerate(list(features.keys())):
rowsup = features[feature] + s + 'sup' + s
rowinf = s + 'inf' + s
for colindex, colvals in enumerate(list(cols.keys())):
celtotalsup = sup[0, indf, colindex]
celtotalinf = inf[0, indf, colindex]
rowsup += celtotalsup + s
rowinf += celtotalinf + s
print(rowsup + ' \\\\')
print(rowinf + ' \\\\')
if True: #TODO correct this if statement...
np.set_printoptions(formatter={'float': '{: 0.2f}'.format})
s = ' & '
r = np.array(np.round(corrs_plot, 2), str)
corr = show
if corrs_plot.shape[0] > 1:
firstrow = "Features" + s + s
for colindex, colvals in enumerate(list(cols.keys())):
firstrow += cols[colvals] + s
firstrow += ' \\\\'
print(firstrow)
for indf, feature in enumerate(list(features.keys())):
for celindex, celvals in enumerate(list(cels.keys())):
rowtotal = features[feature] + s + cels[
celvals] + s + corr + s
for colindex, colvals in enumerate(list(cols.keys())):
rowtotal += r[celindex, indf, colindex] + s
print(rowtotal + ' \\\\')
else:
firstrow = "Features" + s
for colindex, colvals in enumerate(list(cols.keys())):
firstrow += cols[colvals] + s
firstrow += ' \\\\'
print(firstrow)
for indf, feature in enumerate(list(features.keys())):
row = features[feature] + s + corr + s
for colindex, colvals in enumerate(list(cols.keys())):
celtotal = r[0, indf, colindex]
row += celtotal + s
print(row + ' \\\\')
# If requested, the plot is supressed now
if supress_plot:
if bootstrap_info['n']:
return {
'corrs': corrs_plot,
'alt_test': alt_test,
'alt_test_confimax': alt_test_confimax,
'alt_test_confimin': alt_test_confimin,
'null_test': null_test,
'null_test_pval': null_test_pval,
'test_apply': test_apply
}
return {'corrs': corrs_plot, 'test_apply': test_apply}
# creating empth plot!
plt.close('all')
figwidth = int((width * 1.) * 2)
figheight = int((height * 1.) * 2)
fig, axis = plt.subplots(nrows=height,
ncols=width,
sharex='col',
sharey='row',
figsize=(figwidth, figheight))
# if width or height == 1 (means 1 column, or 1 row) axis has only one
# dimension, which make some problems, so it must be reshaped
if height == 1 or width == 1:
axis = axis.reshape(height, width)
# Creatin the colormap and mapping the correlation values in the colors
cmap = matplotlib.cm.get_cmap('coolwarm')
normalize = matplotlib.colors.Normalize(vmin=cb_info['min'],
vmax=cb_info['max'])
colors = [cmap(normalize(value)) for value in corrs_plot]
colors = np.array(colors)
# label sizes:
axis_title_font_size = 30 * scalefont
axis_label_font_size = 25 * scalefont
tick_label_font_size = 25 * scalefont
anotation_font_size = 20
marker_size = 50
# Symbols/markers, lines,
slines = ['-', '--', ':', '-.'] * 5
scolors = ['y', 'g', 'm', 'c', 'b', 'r'] * 5
smarker = ['o', 's', 'D', '^', '*', 'o', 's', 'x', 'D', '+', '^', 'v', '>']
# Adding the scatterplos and linear models
angular_parameter = np.zeros([depth, height, width])
for indf, feature in enumerate(list(features.keys())):
for colindex, colvals in enumerate(list(cols.keys())):
for celindex, celvals in enumerate(list(cels.keys())):
try:
group = grouped.get_group((colvals, celvals))
except KeyError:
continue
# if ((not all(group[feature] == 0.0))
# and (not all(np.isnan(group[feature])))):
datax, datay = tonparray(group[mainprop], group[feature])
if datax.tolist():
if test_apply[celindex, indf, colindex]:
# Linear Regresion
degreee = 1
parameters = np.polyfit(datax, datay, degreee)
fit_fn = np.poly1d(parameters)
angular_parameter[celindex, indf,
colindex] = parameters[0]
# variavel auxiliar pra nao plotar o linha obtida na
# regressao alem dos dados do set (isso pode acontecer
# para as variaveisb2 onde nem todos os samples
# apresentam dados)
yfited_values = np.array(fit_fn(datax))
argmin = np.argmin(datax)
argmax = np.argmax(datax)
trend_x = datax[[argmin, argmax]]
trend_y = yfited_values[[argmin, argmax]]
#print(colvals,celvals,len(datax),len(datay))
# plotando linha obtida com dados da regressao
axis[indf, colindex].plot(trend_x,
trend_y,
marker=None,
linestyle=slines[celindex],
color='k')
# plotando dados da celula
axis[indf, colindex].scatter(datax,
datay,
marker=smarker[celindex],
s=marker_size,
linestyle='None',
label=cels[celvals],
color=colors[celindex, indf,
colindex],
alpha=0.8)
if cels[celvals]:
axis[indf, colindex].legend()
axis[indf, colindex].xaxis.set_tick_params(direction='in',
length=5,
width=0.9)
axis[indf, colindex].yaxis.set_tick_params(direction='in',
length=5,
width=0.9)
# Ajuste do alinhamento dos labels, quantidade de casa deciamais,
axis[0, colindex].xaxis.set_label_position("top")
axis[0, colindex].set_xlabel(cols[colvals],
va='center',
ha='center',
labelpad=15,
size=axis_label_font_size)
axis[indf, 0].set_ylabel(features[feature],
va='center',
ha='center',
labelpad=40,
size=axis_label_font_size,
rotation=60)
for tikslabel in axis[indf, 0].yaxis.get_ticklabels():
tikslabel.set_fontsize(tick_label_font_size)
for tikslabel in axis[-1, colindex].xaxis.get_ticklabels():
tikslabel.set_fontsize(tick_label_font_size)
tikslabel.set_rotation(60)
#y = label['ticklabelssprecision'][1][indf]
#x = label['ticklabelssprecision'][0]
#print(list(axis[indf, colindex].xaxis.get_ticklabels()))
#axis[indf, colindex].xaxis.set_major_formatter(FormatStrFormatter('%0.'+str(x)+'f'))
#axis[indf, colindex].yaxis.set_major_formatter(FormatStrFormatter('%0.'+str(y)+'f'))
#print(list(axis[indf, colindex].xaxis.get_ticklabels()))
#axis[indf, colindex].xaxis.set_major_locator(plt.MaxNLocator(3))
#axis[indf, colindex].yaxis.set_major_locator(plt.MaxNLocator(3))
#print(list(axis[indf, colindex].xaxis.get_ticklabels()))
#axis[indf, colindex].xaxis.set_ticklabels(axis[indf, colindex].xaxis.get_ticklabels(), {'fontweight':'bold'})
#axis[indf, colindex].yaxis.set_ticklabels(axis[indf, colindex].yaxis.get_ticklabels(), {'fontweight':'bold'})
#axis[indf, colindex].xaxis.set_major_formatter(width='bold')
#axis[indf, colindex].yaxis.set_major_formatter(width='bold')
# Colorbar, pra aprensetar as corres das correlacoes
cax, _ = matplotlib.colorbar.make_axes(axis[0, 0],
orientation='vertical',
shrink=80.,
ancor=(2., 2.),
pancor=False)
cbar = matplotlib.colorbar.ColorbarBase(cax, cmap=cmap, norm=normalize)
cax.set_position([0.93, 0.1, 0.04, 0.8])
cax.set_aspect(40) # boxY/boxX
cbar.ax.tick_params(labelsize=tick_label_font_size, labelrotation=90)
plt.subplots_adjust(left=0.125,
right=0.92,
bottom=0.1,
top=0.9,
wspace=0.0,
hspace=0.0)
# Defining what will be ploted
if show == 'test': # The result of the test
truefalse = {True: 'T', False: 'F'}
binfo_plot = np.vectorize(
lambda x, y: truefalse[x] + ',' + truefalse[y])(null_test,
alt_test)
if show == 'testred':
def auxfunc(x, y):
if not x and y:
return 'x'
if x and not y:
return 'o'
return '+'
binfo_plot = np.vectorize(auxfunc)(null_test, alt_test)
if show == 'confint': # The confidence intervals
binfo_plot = np.vectorize(
lambda x, y: str(round(x, 2)) + ',' + str(round(y, 2)))(
alt_test_confimax, alt_test_confimin)
if show == 'pval': # the p-value
binfo_plot = np.array(np.round(null_test_pval, 5), dtype=str)
if show == 'ang': # the angle of the linear model
binfo_plot = np.array(np.round(angular_parameter, 2), dtype=str)
if bootstrap_info['n'] and show in ['pval', 'test', 'ang', 'confint']:
for findex, feature in enumerate(features):
for colindex, colvals in enumerate(list(cols.keys())):
for celindex, celvals in enumerate(list(cels.keys())):
if not test_apply[celindex, findex, colindex]:
binfo_plot[celindex, findex, colindex] = ''
print(binfo_plot)
for indf, feature in enumerate(features):
for colindex in range(width):
for celindex in range(depth):
if test_apply[celindex, indf, colindex]:
bbox = dict(facecolor=scolors[celindex], alpha=0.1)
ypos = 0.155 + (depth - celindex - 1) * 0.2
axis[indf,
colindex].text(0.06,
ypos,
binfo_plot[celindex, indf,
colindex],
fontsize=anotation_font_size,
transform=axis[indf,
colindex].transAxes,
bbox=bbox)
if bootstrap_info['n'] and show in ['testred']:
for findex, feature in enumerate(features):
for colindex, colvals in enumerate(list(cols.keys())):
for celindex, celvals in enumerate(list(cels.keys())):
if not test_apply[celindex, findex, colindex]:
binfo_plot[celindex, findex, colindex] = ' '
print(binfo_plot)
for indf, feature in enumerate(features):
for colindex in range(width):
text = ''
for celindex in range(depth):
text += binfo_plot[celindex, indf, colindex]
if celindex < depth - 1:
text += ','
if np.any(test_apply[:, indf, colindex]):
bbox = dict(facecolor=scolors[0], alpha=0.01)
ypos = 0.155 + (depth - celindex - 1) * 0.2
axis[indf,
colindex].text(0.06,
ypos,
text,
fontsize=anotation_font_size,
transform=axis[indf,
colindex].transAxes,
bbox=bbox)
# Adicionando os principais captions da figura.
fig.text(0.01,
0.524,
label['y'],
ha='center',
rotation='vertical',
size=axis_title_font_size)
fig.text(0.5, 0.95, label['title'], ha='center', size=axis_title_font_size)
fig.text(0.5, 0.01, label['x'], ha='center', size=axis_title_font_size)
cbar.set_label(cb_info['label'], size=axis_title_font_size)
print(list(axis[0, 0].yaxis.get_ticklabels()))
# Salvando a figura para um arquivo
plt.savefig(figure_name, dpi=300)
if bootstrap_info['n']:
return {
'fig': fig,
'axis': axis,
'corrs': corrs_plot,
'alt_test': alt_test,
'alt_test_confimax': alt_test_confimax,
'alt_test_confimin': alt_test_confimin,
'null_test': null_test,
'null_test_pval': null_test_pval,
'angular_parameter': angular_parameter,
'test_apply': test_apply
}
return {
'fig': fig,
'axis': axis,
'corrs': corrs_plot,
'angular_parameter': angular_parameter,
'test_apply': test_apply
}
def plot_3d_point_cloud(x,
y,
z,
show=True,
show_axis=False,
in_u_sphere=False,
marker='.',
s=10,
alpha=.8,
figsize=(2.56, 2.56),
elev=10,
azim=240,
axis=None,
title=None,
filename=None,
colorize=None,
*args,
**kwargs):
if axis is None:
fig = plt.figure(figsize=figsize)
ax = fig.add_subplot(111, projection='3d')
else:
ax = axis
fig = axis
if title is not None:
plt.title(title)
if colorize is not None:
cm = plt.get_cmap(colorize)
col = [cm(float(i) / (x.shape[0])) for i in range(x.shape[0])]
sc = ax.scatter(x,
y,
z,
marker=marker,
s=s,
alpha=alpha,
c=col,
*args,
**kwargs)
else:
sc = ax.scatter(x,
y,
z,
marker=marker,
s=s,
alpha=alpha,
*args,
**kwargs)
# sc = ax.scatter(x, y, z, marker=marker, s=s, alpha=alpha, *args, **kwargs)
ax.view_init(elev=elev, azim=azim)
if in_u_sphere:
ax.set_xlim3d(-0.5, 0.5)
ax.set_ylim3d(-0.5, 0.5)
ax.set_zlim3d(-0.5, 0.5)
else:
# Multiply with 0.7 to squeeze free-space.
miv = 0.7 * np.min([np.min(x), np.min(y), np.min(z)])
mav = 0.7 * np.max([np.max(x), np.max(y), np.max(z)])
ax.set_xlim(miv, mav)
ax.set_ylim(miv, mav)
ax.set_zlim(miv, mav)
#plt.tight_layout()
if not show_axis:
plt.axis('off')
if 'c' in kwargs:
plt.colorbar(sc)
if filename is not None:
plt.savefig(filename)
if show:
plt.show()
plt.close('all')
return fig
def bstalt(data_x,
data_y,
corr_method=comp_spearman,
alpha=0.05,
nresamp=2000,
hist=''):
"""This function bootstrap the Spearaman rank correlation.
The bootstraped sample configurations that present all elements equal are
not considered, because the correlations can\'t be calculated.
Parameters
----------
data_x, datay : numpy arrays (n,) shaped.
Paired data to analyse.
corr_method : a function (default = comp_spearman).
A function that takes two sets of points (x,y in np arrays)
and return its correlation.
alpha : float. (optional, default=0.05)
The confidence limit.
nresamp : intiger. (optional, default=2000)
The quantity of data resamples in the procedure.
hist : string (optional, default='').
If hist == 'plot' a figure with data result histogram will be
displayed on screem, otherwise the same figure will be saved to a
file named hist + '.png'.
Return
------
reject_null : boolean.
True if the null hypothese could be rejected withing the
confidence level.
Example
------
>>> data_y = np.array([0.29210368, 0.09100691, 0.03445345, 0.1953896 ,
0.09828076, 0.06194474, 0.07301951, 0.05899114,
0.05012644, 0.03095898, 0.10257979, 0.08892738,
0.05457695, 0.02178669, 0.0326735 ])
>>> data_x = np.array([-4.38 , -3.9418, -4.0413, -4.1549, -4.2052,
-3.915 , -4.1796, -4.1815, -3.972 , -4.0494,
-4.2255, -4.2772, -3.9947, -3.9589, -3.8393])
>>> bootstraping_spearmancorr(data_x, data_y)
True
"""
rs = corr_method(data_x, data_y) # original data correlation
data = np.zeros(nresamp) # the data will be stored in this variable
possible_data = np.array(range(0, len(data_x))) # auxiliar variable
interation = 0 # auxiliar variable
while interation < nresamp:
# resampling pairs with replacement:
resampled_pairs = resample(possible_data)
resampled_data_x = data_x[resampled_pairs]
resampled_data_y = data_y[resampled_pairs]
# to guarantee that the elements are not all equal
if np.all(resampled_data_x == resampled_data_x[0]):
continue
if np.all(resampled_data_y == resampled_data_y[0]):
continue
# calculating correlation for the resampled data
boostrapted_corr = corr_method(resampled_data_x, resampled_data_y)
# storing the correlacao
data[interation] = boostrapted_corr
interation += 1
# Sorting data
data.sort()
index_lower_confidence = int(round(nresamp * alpha / 2.))
index_upper_confidence = int(round(nresamp - nresamp * alpha / 2.))
confidence_data = data[index_lower_confidence:index_upper_confidence]
confidence_interval = [confidence_data[0], confidence_data[-1]]
# H0 is rejected if 0 is within the confidence interval:
reject_null = np.all(np.sign(confidence_data) == np.sign(rs))
if hist != '':
plt.close('all')
plt.ylabel('Frequancy')
plt.xlabel('Correlation Coefficient')
plt.xlim(-1.02, 1.02)
bins = 201
ranges = (-1., 1.)
plt.hist(confidence_data,
bins=bins,
range=ranges,
label="Bootstraped Data in the CI")
plt.hist(data,
bins=bins,
histtype='step',
range=ranges,
label="Bootstraped Data")
plt.plot([rs, rs],
[0, np.histogram(data, bins=bins, range=ranges)[0].max()],
label="Sample Correlation")
plt.plot([0, 0],
[0, np.histogram(data, bins=bins, range=ranges)[0].max()],
label="Correlation = 0")
plt.legend()
# ploting or saving to a file:
if hist == 'plot':
plt.show()
else:
plt.savefig(hist + ".png")
return reject_null, confidence_interval
def run_one_step(self):
""" """
# find the faulted node with the largest drainage area.
largest_da = np.max(self._model.grid.at_node['drainage_area'][
self._model.boundary_handler['NormalFault'].faulted_nodes == True])
largest_da_ind = np.where(
self._model.grid.at_node['drainage_area'] == largest_da)[0][0]
start_node = self._model.grid.at_node['flow__receiver_node'][
largest_da_ind]
(profile_IDs, dists_upstr) = analyze_channel_network_and_plot(
self._model.grid,
number_of_channels=1,
starting_nodes=[start_node],
create_plot=False)
elevs = model.z[profile_IDs]
self.relative_times.append(self._model.model_time /
model.params['run_duration'])
offset = np.min(elevs[0])
max_distance = np.max(dists_upstr[0][0])
self.channel_segments.append(
np.array((dists_upstr[0][0], elevs[0] - offset)).T)
self.xnormalized_segments.append(
np.array((dists_upstr[0][0] / max_distance, elevs[0] - offset)).T)
self.relative_times.append(self._model.model_time /
model.params['run_duration'])
colors = cm.viridis_r(self.relative_times)
xmin = [xy.min(axis=0)[0] for xy in self.channel_segments]
ymin = [xy.min(axis=0)[1] for xy in self.channel_segments]
xmax = [xy.max(axis=0)[0] for xy in self.channel_segments]
ymax = [xy.max(axis=0)[1] for xy in self.channel_segments]
fs = (8, 6)
fig, ax = plt.subplots(figsize=fs, dpi=300)
ax.set_xlim(0, max(xmax))
ax.set_ylim(0, max(ymax))
line_segments = LineCollection(self.channel_segments,
colors=colors,
linewidth=0.5)
ax.add_collection(line_segments)
yr = str(self._model.model_time / (1e6)).zfill(4)
plt.savefig('profile_' + yr + '.png')
plt.close()
fig, ax = plt.subplots(figsize=fs, dpi=300)
ax.set_xlim(0, 1)
ax.set_ylim(0, max(ymax))
line_segments = LineCollection(self.xnormalized_segments,
colors=colors,
linewidth=0.5)
ax.add_collection(line_segments)
yr = str(self._model.model_time / (1e6)).zfill(4)
plt.savefig('normalized_profile_' + yr + '.png')
plt.close()
plt.figure()
plot_channels_in_map_view(self._model.grid, profile_IDs)
plt.savefig('topography_' + yr + '.png')
plt.close()
plt.figure()
imshow_grid(model.grid,
model.grid.at_node['soil__depth'],
cmap='viridis',
limits=(0, 15))
plt.savefig('soil_' + yr + '.png')
plt.close()
plt.figure()
imshow_grid(self._model.grid,
self._model.grid.at_node['sediment__flux'],
cmap='viridis')
plt.savefig('sediment_flux_' + yr + '.png')
plt.close()
U_eff = U_fast + U_back
U_eff_slow = U_slow + U_back
area = np.sort(self._model.grid.at_node['drainage_area'][
self._model.boundary_handler['NormalFault'].faulted_nodes == True])
area = area[area > 0]
little_q = (
area *
self._model.params['runoff_rate'])**self._model.params['m_sp']
#area_to_the_m = area ** self._model.params['m_sp']
detachment_prediction = (
(U_eff / (self._model.params['K_rock_sp']))
**(1.0 / self._model.params['n_sp']) *
(1.0 / little_q)**(1.0 / self._model.params['n_sp']))
transport_prediction = (
((U_eff * self._model.params['v_sc']) /
(self._model.params['K_sed_sp'] *
self._model.params['runoff_rate'])) +
((U_eff) / (self._model.params['K_sed_sp'])))**(
1.0 / self._model.params['n_sp']) * (
(1.0 / little_q)**(1.0 / self._model.params['n_sp']))
space_prediction = (
((U_eff * self._model.params['v_sc']) * (1.0 - Ff) /
(self._model.params['K_sed_sp'] *
self._model.params['runoff_rate'])) +
((U_eff) / (self._model.params['K_rock_sp'])))**(
1.0 / self._model.params['n_sp']) * (
(1.0 / little_q)**(1.0 / self._model.params['n_sp']))
detachment_prediction_slow = (
(U_eff_slow / (self._model.params['K_rock_sp']))
**(1.0 / self._model.params['n_sp']) *
(1.0 / little_q)**(1.0 / self._model.params['n_sp']))
transport_prediction_slow = (
((U_eff_slow * self._model.params['v_sc']) /
(self._model.params['K_sed_sp'] *
self._model.params['runoff_rate'])) +
((U_eff_slow) / (self._model.params['K_sed_sp'])))**(
1.0 / self._model.params['n_sp']) * (
(1.0 / little_q)**(1.0 / self._model.params['n_sp']))
space_prediction_slow = (
((U_eff_slow * self._model.params['v_sc']) * (1.0 - Ff) /
(self._model.params['K_sed_sp'] *
self._model.params['runoff_rate'])) +
((U_eff_slow) / (self._model.params['K_rock_sp'])))**(
1.0 / self._model.params['n_sp']) * (
(1.0 / little_q)**(1.0 / self._model.params['n_sp']))
# TODO need to fix space predictions here to include new soil thickness.
fs = (8, 6)
fig, ax = plt.subplots(figsize=fs, dpi=300)
plt.plot(area,
detachment_prediction,
'c',
lw=5,
label='Detachment Prediction')
plt.plot(area, transport_prediction, 'b', label='Transport Prediction')
plt.plot(area, space_prediction, 'm', label='Space Prediction')
plt.plot(area, detachment_prediction_slow, 'c', lw=5, alpha=0.3)
plt.plot(area, transport_prediction_slow, 'b', alpha=0.3)
plt.plot(area, space_prediction_slow, 'm', alpha=0.3)
plt.plot(self._model.grid.at_node['drainage_area'][
self._model.boundary_handler['NormalFault'].faulted_nodes == True],
self._model.grid.at_node['topographic__steepest_slope']
[self._model.boundary_handler['NormalFault'].faulted_nodes ==
True],
'k.',
label='Fault Block Nodes')
plt.plot(self._model.grid.at_node['drainage_area']
[self._model.boundary_handler['NormalFault'].faulted_nodes ==
False],
self._model.grid.at_node['topographic__steepest_slope']
[self._model.boundary_handler['NormalFault'].faulted_nodes ==
False],
'r.',
label='Unfaulted Nodes')
plt.plot(self._model.grid.at_node['drainage_area'][profile_IDs],
self._model.grid.at_node['topographic__steepest_slope']
[profile_IDs],
'g.',
label='Main Channel Nodes')
plt.legend()
ax.set_xscale('log')
ax.set_yscale('log')
plt.xlabel('log 10 Area')
plt.ylabel('log 10 Slope')
plt.savefig('slope_area_' + yr + '.png')
plt.close()
def run_analysis(idx, fdr=0.2, **kwargs):
np.random.seed(8 + idx)
torch.manual_seed(8 + idx)
print('Generating synthetic covariates')
X = generate_synthetic_X(**kwargs)
print('Getting synthetic response')
z, h_true, signal_indices, coefficients = generate_synthetic_z(X, **kwargs)
if h_true.sum() == 0:
print('WARNING: no signals!')
raise Exception()
print(
f'{h_true.sum()} true positives, {(~h_true).sum()} nulls, and {len(signal_indices)} nonnull features.'
)
direc = 'pure-synthetic'
if not os.path.exists(f'data/{direc}'):
os.makedirs(f'data/{direc}')
#### Two-groups empirical bayes model ####
print('Stage 1: Creating blackbox 2-groups model')
fdr_model = BlackBoxTwoGroupsModel(X, z, fdr=fdr, estimate_null=True)
print('Training')
sys.stdout.flush()
results = fdr_model.train(save_dir=f'data/{direc}/twogroups',
verbose=False,
batch_size=None,
num_folds=5,
num_epochs=100)
# Save the Stage 1 significant experimental outcome results
h_predictions = results['predictions']
bh_preds = bh_predictions(
p_value_2sided(z,
mu0=fdr_model.null_dist[0],
sigma0=fdr_model.null_dist[1]), fdr)
#### Posterior EB knockoffs model ####
print('Stage 2: Empirical Bayes knockoffs')
crt = PosteriorConditionalRandomizationTester(fdr_model, fdr=fdr)
# Run a CRT for each feature
crt.run(verbose=False)
print('Getting the predictions')
crt_results = crt.predictions()
t_crt = crt_results['tstats']
h_crt = crt_results['discoveries']
# Try the model-X knockoffs approach using the same knockoff samples
from knockoffs import knockoff_filter
knockoff_preds = np.zeros(len(crt.tstats), dtype=bool)
true_tstat = (
fdr_model.posteriors * np.log(fdr_model.posteriors) +
(1 - fdr_model.posteriors) * np.log(1 - fdr_model.posteriors)).mean()
true_tstat -= crt.tstats_mean
true_tstat /= crt.tstats_std
plt.hist(true_tstat - crt.tstats, bins=30)
plt.savefig('plots/knockoffs-temp.pdf', bbox_inches='tight')
plt.close()
knockoff_preds[knockoff_filter(true_tstat - crt_results['tstats'],
fdr,
offset=1.0)] = True
# Save everything to file
np.save(f'data/{direc}/h_predictions_{idx}.npy', h_predictions)
np.save(f'data/{direc}/bh_predictions_{idx}.npy', bh_preds)
np.save(f'data/{direc}/feature_predictions_{idx}.npy', h_crt)
np.save(f'data/{direc}/h_priors_{idx}.npy', fdr_model.priors)
np.save(f'data/{direc}/h_posteriors_{idx}.npy', fdr_model.posteriors)
np.save(f'data/{direc}/z_empirical_null_{idx}.npy', fdr_model.null_dist)
np.save(f'data/{direc}/z_alternative_{idx}.npy',
[fdr_model.alt_dist.x, fdr_model.alt_dist.y])
np.save(f'data/{direc}/knockoff_predictions_{idx}.npy', knockoff_preds)
np.save(f'data/{direc}/knockoff_empirical_null_{idx}.npy',
[crt.null_dist.bins, crt.null_dist.w])
np.save(f'data/{direc}/knockoff_alternative_{idx}.npy',
[crt.alt_dist.bins, crt.alt_dist.w])
np.save(f'data/{direc}/knockoff_prior_{idx}.npy', [crt.pi0])
np.save(f'data/{direc}/knockoff_posteriors_{idx}.npy', crt.posteriors)
# Save the ground truth
np.save(f'data/{direc}/h_true_{idx}.npy', h_true)
np.save(f'data/{direc}/signal_indices_{idx}.npy', signal_indices)
np.save(f'data/{direc}/signal_coefs_{idx}.npy', coefficients)
# Report results
tpp1_debt = (h_true & h_predictions).sum() / max(1, h_true.sum())
tpp1_bh = (h_true & bh_preds).sum() / max(1, h_true.sum())
tpp2_debt = len([s for s in signal_indices if h_crt[s]
]) / len(signal_indices)
tpp2_knockoffs = len([s for s in signal_indices if knockoff_preds[s]
]) / len(signal_indices)
fdp1_debt = ((~h_true) & h_predictions).sum() / max(1, h_predictions.sum())
fdp1_bh = ((~h_true) & bh_preds).sum() / max(1, bh_preds.sum())
fdp2_debt = len([
s for s, h in enumerate(h_crt) if h and s not in signal_indices
]) / max(1, h_crt.sum())
fdp2_knockoffs = len([
s
for s, h in enumerate(knockoff_preds) if h and s not in signal_indices
]) / max(1, knockoff_preds.sum())
print('')
print(
f'DEBT discoveries: {h_predictions.sum()} TPP: {tpp1_debt*100:.2f}% FDP: {fdp1_debt*100:.2f}%'
)
print(
f'BH discoveries: {bh_preds.sum()} TPP: {tpp1_bh*100:.2f}% FDP: {fdp1_bh*100:.2f}%'
)
print(
f'DEBT features: {h_crt.sum()} TPP: {tpp2_debt*100:.2f}% FDP: {fdp2_debt*100:.2f}%'
)
print(
f'Knockoffs features: {knockoff_preds.sum()} TPP: {tpp2_knockoffs*100:.2f}% FDP: {fdp2_knockoffs*100:.2f}%'
)
def plot_triangle(sim_samples,
gp_samples,
burnin_frac=0.1,
emulator=True,
gp_error=False):
if gp_error and emulator:
label_gp = 'GP (Error)'
elif emulator and not gp_error:
label_gp = 'GP (Mean)'
else:
label_gp = 'Simulator (MOPED)'
ndim = sim_samples.shape[-1]
names = ["x%s" % i for i in range(ndim)]
labels = [
r"\Omega_{m}", r"w_{0}", r"M_{B}", r"\delta M", r"\alpha", r"\beta"
]
# for the simulator
burnin = int(burnin_frac * sim_samples.shape[1])
samples_exact = sim_samples[:, burnin:, :].reshape((-1, ndim))
cut_samps = samples_exact[samples_exact[:, 0] >= 0.0, :]
samples1 = MCSamples(samples=cut_samps,
names=names,
labels=labels,
ranges={'x0': (0.0, None)})
# for the emulator
burnin = int(burnin_frac * gp_samples.chain.shape[1])
samples_emu = gp_samples.chain[:, burnin:, :].reshape((-1, ndim))
cut_samps = samples_emu[samples_emu[:, 0] >= 0.0, :]
samples2 = MCSamples(samples=cut_samps,
names=names,
labels=labels,
ranges={'x0': (0.0, None)})
# setups for plotting
sim_color = '#EEC591'
gp_color = 'Blue'
alpha_tri = 0.1
red_patch = mpatches.Patch(color=sim_color,
label='Simulator',
alpha=alpha_tri)
gp_line = Line2D([0], [0],
color=gp_color,
linewidth=3,
linestyle='--',
label=label_gp)
rec_leg = [red_patch, gp_line]
contours = np.array([0.68, 0.95])
G = plots.getSubplotPlotter(subplot_size=3.5)
samples1.updateSettings({'contours': [0.68, 0.95]})
G.triangle_plot([samples1],
filled=True,
line_args={
'lw': 3,
'color': sim_color
},
contour_colors=[sim_color])
G.settings.num_plot_contours = 2
plt.legend(handles=rec_leg,
loc='best',
prop={'size': 25},
bbox_to_anchor=(0.7, 6.0),
borderaxespad=0.)
G.settings.alpha_filled_add = alpha_tri
for i in range(0, 6):
for j in range(0, i + 1):
if i != j:
ax = G.subplots[i, j]
a, b = G.get_param_array(samples2,
['x' + str(j), 'x' + str(i)])
density = G.sample_analyser.get_density_grid(samples2, a, b)
density.contours = density.getContourLevels(contours)
contour_levels = density.contours
ax.contour(density.x,
density.y,
density.P,
sorted(contour_levels),
colors=gp_color,
linewidths=3,
linestyles='--')
ax.tick_params(labelsize=20)
ax.yaxis.label.set_size(20)
ax.xaxis.label.set_size(20)
else:
ax = G.subplots[i, j]
dense = samples2.get1DDensity('x' + str(i))
dense.normalize(by='max')
ax.plot(dense.x, dense.P, lw=3, c=gp_color, linestyle='--')
ax.tick_params(labelsize=20)
ax.yaxis.label.set_size(20)
ax.xaxis.label.set_size(20)
plt.savefig('images/triangle_plot.jpg',
bbox_inches='tight',
transparent=False)
plt.close()
def kohonen():
"""Example for using create_data, plot_data and som_step.
"""
plb.close('all')
dim = 28 * 28
data_range = 255.0
# load in data and labels
data = np.array(np.loadtxt('data.txt'))
labels = np.loadtxt('labels.txt')
# select 4 digits
name = 'Seth Vanderwilt' # REPLACE BY YOUR OWN NAME
targetdigits = name2digits(
name) # assign the four digits that should be used
print(targetdigits) # output the digits that were selected
# this selects all data vectors that corresponds to one of the four digits
data = data[np.logical_or.reduce([labels == x for x in targetdigits]), :]
# get the label for each data vector corresponding to one of the four digits
labels = labels[np.logical_or.reduce([labels == x for x in targetdigits])]
dy, dx = data.shape
#set the size of the Kohonen map. In this case it will be 6 X 6
size_k = 6 # default 6, also tried 7, 8, 10
#set the width of the neighborhood via the width of the gaussian that
#describes it
sigma = 3.0 # default 3, also tried 0.5, 1, 2, 5
#initialise the centers randomly
centers = np.random.rand(size_k**2, dim) * data_range
#build a neighborhood matrix
neighbor = np.arange(size_k**2).reshape((size_k, size_k))
#set the learning rate
eta = 0.5 # HERE YOU HAVE TO SET YOUR OWN LEARNING RATE
#set the maximal iteration count
tmax = 10000 # this might or might not work; use your own convergence criterion
#tmax = 500 # this might or might not work; use your own convergence criterion
#set the random order in which the datapoints should be presented
i_random = np.arange(tmax) % dy
np.random.shuffle(i_random)
# NOTE change to false if not on question 5
decreasing_width = True
print("initial sigma: " + str(sigma))
for t, i in enumerate(i_random):
if decreasing_width:
sigma *= 0.9999 # decrease by 0.1%
som_step(centers, data[i, :], neighbor, eta, sigma)
print("final sigma: " + str(sigma))
# Our centers
print(centers)
# NOTE assign each center the label of the nearest datapoint
assigned_digit = []
for ci in range(len(centers)):
nearest_datapoint = np.argmin(np.sum((centers[ci] - data[:])**2, 1))
# Get label of nearest datapoint
assigned_digit.append(int(labels[nearest_datapoint]))
# for visualization, you can use this:
for i in range(size_k**2):
ax = plb.subplot(size_k, size_k, i + 1)
ax.set_title(assigned_digit[i])
plb.imshow(np.reshape(centers[i, :], [28, 28]),
interpolation='bilinear')
plb.axis('off')
# fix display problem
plb.subplots_adjust(hspace=0.5)
# leave the window open at the end of the loop
plb.show()
plb.draw()
def shap_deep_explainer(self,
model_no,
num_reference,
img_input,
norm_reverse=True,
blend_original_image=False,
gif_fps=1,
ranked_outputs=1,
base_dir_save='/tmp/DeepExplain'):
# region mini-batch because of GPU memory limitation
list_shap_values = []
batch_size = self.dicts_models[model_no]['batch_size']
split_times = math.ceil(num_reference / batch_size)
for i in range(split_times):
#shap 0.26
#shap 0.4, check_additivity=False
# shap_values_tmp1 = self.list_e[model_no][i].shap_values(img_input, ranked_outputs=ranked_outputs,
# check_additivity=check_additivity)
shap_values_tmp1 = self.list_e[model_no][i].shap_values(
img_input,
ranked_outputs=ranked_outputs,
)
# shap_values ranked_outputs
# [0] [0] (1,299,299,3)
# [1] predict_class array
shap_values_copy = copy.deepcopy(shap_values_tmp1)
list_shap_values.append(shap_values_copy)
for i in range(ranked_outputs):
for j in range(len(list_shap_values)):
if j == 0:
shap_values_tmp2 = list_shap_values[0][0][i]
else:
shap_values_tmp2 += list_shap_values[j][0][i]
shap_values_results = copy.deepcopy(list_shap_values[0])
shap_values_results[0][i] = shap_values_tmp2 / split_times
# endregion
# region save files
str_uuid = str(uuid.uuid1())
list_classes = []
list_images = []
for i in range(ranked_outputs):
predict_class = int(
shap_values_results[1][0][i]) # numpy int 64 - int
list_classes.append(predict_class)
save_filename = os.path.join(
base_dir_save, str_uuid,
'Shap_Deep_Explainer{}.jpg'.format(predict_class))
os.makedirs(os.path.dirname(save_filename), exist_ok=True)
list_images.append(save_filename)
pred_class_num = len(shap_values_results[0])
if blend_original_image:
if norm_reverse:
img_original = np.uint8(input_norm_reverse(img_input[0]))
else:
img_original = np.uint8(img_input[0])
img_original_file = os.path.join(os.path.dirname(list_images[0]),
'deepshap_original.jpg')
cv2.imwrite(img_original_file, img_original)
for i in range(pred_class_num):
# predict_max_class = attributions[1][0][i]
attribution1 = shap_values_results[0][i]
# attributions.shape: (1, 299, 299, 3)
data = attribution1[0]
data = np.mean(data, -1)
abs_max = np.percentile(np.abs(data), 100)
abs_min = abs_max
# dx, dy = 0.05, 0.05
# xx = np.arange(0.0, data1.shape[1], dx)
# yy = np.arange(0.0, data1.shape[0], dy)
# xmin, xmax, ymin, ymax = np.amin(xx), np.amax(xx), np.amin(yy), np.amax(yy)
# extent = xmin, xmax, ymin, ymax
# cmap = 'RdBu_r'
# cmap = 'gray'
cmap = 'seismic'
plt.axis('off')
# plt.imshow(data1, extent=extent, interpolation='none', cmap=cmap, vmin=-abs_min, vmax=abs_max)
# plt.imshow(data, interpolation='none', cmap=cmap, vmin=-abs_min, vmax=abs_max)
# fig = plt.gcf()
# fig.set_size_inches(2.99 / 3, 2.99 / 3) # dpi = 300, output = 700*700 pixels
plt.gca().xaxis.set_major_locator(plt.NullLocator())
plt.gca().yaxis.set_major_locator(plt.NullLocator())
plt.subplots_adjust(top=1,
bottom=0,
right=1,
left=0,
hspace=0,
wspace=0)
plt.margins(0, 0)
if blend_original_image:
plt.imshow(data,
interpolation='none',
cmap=cmap,
vmin=-abs_min,
vmax=abs_max)
save_filename1 = list_images[i]
plt.savefig(save_filename1, bbox_inches='tight', pad_inches=0)
plt.close()
img_heatmap = cv2.imread(list_images[i])
(tmp_height, tmp_width) = img_original.shape[:-1]
img_heatmap = cv2.resize(img_heatmap, (tmp_width, tmp_height))
img_heatmap_file = os.path.join(
os.path.dirname(list_images[i]),
'deepshap_{0}.jpg'.format(i))
cv2.imwrite(img_heatmap_file, img_heatmap)
dst = cv2.addWeighted(img_original, 0.65, img_heatmap, 0.35, 0)
img_blend_file = os.path.join(
os.path.dirname(list_images[i]),
'deepshap_blend_{0}.jpg'.format(i))
cv2.imwrite(img_blend_file, dst)
# region create gif
import imageio
mg_paths = [
img_original_file, img_heatmap_file, img_blend_file
]
gif_images = []
for path in mg_paths:
gif_images.append(imageio.imread(path))
img_file_gif = os.path.join(os.path.dirname(list_images[i]),
'deepshap_{0}.gif'.format(i))
imageio.mimsave(img_file_gif, gif_images, fps=gif_fps)
list_images[i] = img_file_gif
# endregion
else:
plt.imshow(data,
interpolation='none',
cmap=cmap,
vmin=-abs_min,
vmax=abs_max)
save_filename1 = list_images[i]
plt.savefig(save_filename1, bbox_inches='tight', pad_inches=0)
plt.close()
# endregion
return list_classes, list_images
def mypltshow(fnfig):
plt.savefig(fnfig)
myshell("sleep 1;gv " + fnfig + "&")
plt.close() #plt.show()
def plot_climate_cflux(cflux_data: Tuple,
climate_data: np.array,
time: np.array,
plot_path: str = ".") -> None:
"""The function plots the carbon flux with climatological data
Args:
cflux_path (str): The path to cflux ouput file.
climate_path (str): The path to climate data input file.
plot_path (str): The path to the ouput graph.
Returns:
None: And plots in the specified folder
"""
av_rain = climate_data[0, :]
av_temp = climate_data[1, :]
av_irradiance = climate_data[2, :]
#fig, (ax1, ax2, ax3, ax4, ax5) = plt.subplots(5,1, figsize=(12,8))
nee_arr, gpp_arr, biomass_arr, deadwood_arr = cflux_data
strt = 0
end = climate_data.shape[1]
end = 2000
av_rain = climate_data[0, strt:end]
av_temp = climate_data[1, strt:end]
av_irradiance = climate_data[2, strt:end]
time = time[strt:end]
# Multiplying by 100 for unit conversion
nee_arr = nee_arr[strt:end] * 100
gpp_arr = gpp_arr[strt:end] * 100
biomass_arr = biomass_arr[strt:end] * 100
deadwood_arr = deadwood_arr[strt:end] * 100
if strt > 0 or end < climate_data.shape[1]:
plot_path = plot_path.split('.')[0] + '_short.' + plot_path.split(
'.')[1]
fig, (ax1, ax3, ax4, ax5, ax6, ax7, ax8) = plt.subplots(7,
1,
figsize=(16, 14))
ax1.plot(time, av_irradiance, color="darkorange")
ax1.set_xlim(left=time[0], right=time[-1])
ax1.set_ylabel("Solar Irradiance [$micro mol$ $s^{-1}$ $m^{-2}$]")
# ax2.plot(time, av_pet)
ax3.plot(time, av_temp, color="indianred")
ax3.set_xlim(left=time[0], right=time[-1])
ax3.set_ylabel(u'Temperature $[\u00B0C]$')
ax4.bar(time, av_rain, color="mediumblue")
ax4.set_xlim(left=time[0], right=time[-1])
ax4.set_ylabel("Precipitation [$mm$ $d^{-1}$]")
# Cflux plots
ax5.plot(time, nee_arr, color="lightblue")
ax5.plot(time, np.mean(nee_arr, axis=1), color="k")
#nee_positive = np.where(nee_extend<0, 0, nee_extend)
#nee_negative = np.where(nee_extend>0, 0, nee_extend)
# ax5.fill_between(time, nee_positive, color = "slateblue")
# ax5.fill_between(time, nee_negative, color = "lightcoral")
ax5.axhline(color="k", linestyle="--")
# ax5.set_ylabel("NEE [$t_C$ $ha^{-1}$ $a^{-1}$]")
ax5.set_ylabel("NEE [$g_C$ $m^{-2}$ $a^{-1}$]")
ax5.set_xlabel("Time [Years]")
ax5.set_xlim(left=time[0], right=time[-1])
# We are doing a custom hline here
y = np.mean(np.mean(gpp_arr, axis=1))
ax6.plot(time, gpp_arr, color="lightblue")
ax6.plot(time, np.mean(gpp_arr, axis=1), color="k")
ax6.axhline(y=y, color="k", linestyle="--")
# ax6.set_ylabel("GPP [$t_C$ $ha^{-1}$ $a^{-1}$]")
ax6.set_ylabel("GPP [$g_C$ $m^{-2}$ $a^{-1}$]")
ax6.set_xlabel("Time [Years]")
ax6.set_xlim(left=time[0], right=time[-1])
y = np.mean(np.mean(biomass_arr, axis=1))
ax7.plot(time, biomass_arr, color="lightblue")
ax7.plot(time, np.mean(biomass_arr, axis=1), color="k")
ax7.axhline(y=y, color="k", linestyle="--")
# ax7.set_ylabel("Cpool_Biomass [$t_C$ $ha^{-1}$]")
ax7.set_ylabel("Cpool_Biomass [$g_C$ $m^{-2}$]")
ax7.set_xlabel("Time [Years]")
ax7.set_xlim(left=time[0], right=time[-1])
y = np.mean(np.mean(deadwood_arr, axis=1))
ax8.plot(time, deadwood_arr, color="lightblue")
ax8.plot(time, np.mean(deadwood_arr, axis=1), color="k")
ax8.axhline(y=y, color="k", linestyle="--")
# ax8.set_ylabel("Cpool_Deadwood [$t_C$ $ha^{-1}$]")
ax8.set_ylabel("Cpool_Deadwood [$g_C$ $m^{-2}$]")
ax8.set_xlabel("Time [Years]")
ax8.set_xlim(left=time[0], right=time[-1])
plt.tight_layout()
plt.savefig(plot_path)
plt.close()
### Another figure
# fig, (ax1, ax2) = plt.subplots(2,1, figsize=(8,8))
# av_gpp = np.mean(gpp_arr, axis =1)
# ax1.scatter(av_gpp, av_temp, color = "rebeccapurple")
# ax1.set_ylabel("av_temp [..]")
# ax1.set_xlabel("gpp [..]")
# ax2.scatter(av_gpp, av_rain, color = "rebeccapurple")
# ax2.set_ylabel("av_rainp [..]")
# ax2.set_xlabel("gpp [..]")
# plt.savefig('plots/scatter.png')
return
def plot_3d_point_cloud(batch_img1, plot_kwargs, *args, **kwargs):
ith = plot_kwargs.get('ith', 0)
epoch = plot_kwargs.get('epoch', -1)
show = plot_kwargs.get('show', False)
show_axis = plot_kwargs.get('show_axis', True)
in_u_sphere = plot_kwargs.get('in_u_sphere', False)
marker = plot_kwargs.get('marker', '.')
s = plot_kwargs.get('s', 8)
alpha = plot_kwargs.get('alpha' , .8)
figsize = plot_kwargs.get('figsize' , (5,5))
elev = plot_kwargs.get('elev' , 10)
azim = plot_kwargs.get('azim' , 240)
axis = plot_kwargs.get('axis' , None)
title = plot_kwargs.get('title' , None)
save = plot_kwargs.get('save' , True)
save_dir = plot_kwargs.get('save_dir' , './')
file_name = plot_kwargs.get('file_name' , None)
x = batch_img1[ith][:, 0]
y = batch_img1[ith][:, 1]
z = batch_img1[ith][:, 2]
if axis is None:
fig = plt.figure(figsize=figsize)
ax = fig.add_subplot(111, projection='3d')
else:
ax = axis
fig = axis
if title is not None:
plt.title(title)
sc = ax.scatter(x, y, z, marker=marker, s=s, alpha=alpha, *args, **kwargs)
ax.view_init(elev=elev, azim=azim)
if in_u_sphere:
ax.set_xlim3d(-0.5, 0.5)
ax.set_ylim3d(-0.5, 0.5)
ax.set_zlim3d(-0.5, 0.5)
else:
miv = 0.7 * np.min([np.min(x), np.min(y), np.min(z)]) # Multiply with 0.7 to squeeze free-space.
mav = 0.7 * np.max([np.max(x), np.max(y), np.max(z)])
ax.set_xlim(miv, mav)
ax.set_ylim(miv, mav)
ax.set_zlim(miv, mav)
plt.tight_layout()
if not show_axis:
plt.axis('off')
if 'c' in kwargs:
plt.colorbar(sc)
if show:
plt.show()
if save:
print(f'image saved at {save_dir}/{file_name}')
plt.savefig(osp.join(save_dir, file_name))
plt.close('all')
# return fig
def plot_qpi_sphere(qpi_real, qpi_sim, path=None, simtype="simulation"):
"""Plot QPI sphere analysis data"""
fig = plt.figure(figsize=(9, 5))
px_um = qpi_real["pixel size"] * 1e6
radius_um = qpi_sim["sim radius"] * 1e6
center = qpi_sim["sim center"]
index = qpi_sim["sim index"]
real_phase = qpi_real.pha
kw_phase = {
"px_um": px_um,
"cbar": True,
"imtype": "phase",
"vmin": real_phase.min(),
"vmax": real_phase.max(),
}
real_inten = qpi_real.amp**2
kw_inten = {
"px_um": px_um,
"cbar": True,
"imtype": "intensity",
"vmin": real_inten.min(),
"vmax": real_inten.max(),
}
# real phase
ax1 = plt.subplot(231, title="data (phase)")
plot_image(data=real_phase, ax=ax1, **kw_phase)
# simulated phase
ax2 = plt.subplot(232, title=simtype + " (phase)")
plot_image(data=qpi_sim.pha, ax=ax2, **kw_phase)
ax2.text(
0.01,
.99,
"index: {:.5f}\n".format(index) + "radius: {:.3f}µm".format(radius_um),
horizontalalignment="left",
verticalalignment="top",
color="w",
transform=ax2.transAxes,
)
# phase residuals
ax3 = plt.subplot(233, title="phase residuals")
errmax = qpi_sim.pha.max() * .2
plot_image(data=qpi_sim.pha - real_phase,
ax=ax3,
imtype="phase error",
vmax=errmax,
vmin=-errmax,
px_um=px_um)
# real intensity
ax4 = plt.subplot(234, title="data (intensity)")
plot_image(data=real_inten, ax=ax4, **kw_inten)
# computed intensity
ax5 = plt.subplot(235)
if len(simtype) > 9:
# sometimes the title is too long and is printed on top of the units
kw5 = {"loc": "right", "ha": "right"}
else:
kw5 = {}
ax5.set_title(simtype + " (intensity)", **kw5)
plot_image(data=qpi_sim.amp**2, ax=ax5, **kw_inten)
# plot detected radius
for ax in [ax1, ax2, ax4, ax5]:
circ = mpl.patches.Circle(
xy=((center[1] + .5) * px_um, (center[0] + .5) * px_um),
radius=radius_um,
facecolor="none",
edgecolor="w",
ls=(0, (3, 8)),
lw=.5,
)
ax.add_patch(circ)
# line plot through center
ax6 = plt.subplot(236, title="phase line plot")
if int(center[0]) >= 0 and int(center[0]) < qpi_sim.shape[0]:
x = np.arange(qpi_real.shape[1]) * px_um
ax6.plot(x, qpi_sim.pha[int(center[0])], label=simtype)
ax6.plot(x, qpi_real.pha[int(center[0])], label="data")
ax6.set_xlabel("[µm]")
ax6.legend(loc="center right")
# remove unused labels
for ax in [ax1, ax2, ax3]:
ax.set_xlabel("")
for ax in [ax2, ax3, ax5]:
ax.set_ylabel("")
plt.tight_layout(rect=(0, 0, 1, .93), pad=.1, h_pad=.6)
# add identifier
fig.text(x=.5,
y=.99,
s=qpi_sim["identifier"],
verticalalignment="top",
horizontalalignment="center",
fontsize=14)
if path:
fig.savefig(path)
plt.close()
else:
return fig
def index(self, document):
inv = obspy.read_inventory(document, format="stationxml")
indices = []
for network in inv:
for station in network:
for channel in station:
if channel.response:
if channel.response.instrument_sensitivity:
_i = channel.response.instrument_sensitivity
total_sensitivity = _i.value
sensitivity_frequency = _i.frequency
units_after_sensitivity = _i.input_units
else:
total_sensitivity = None
sensitivity_frequency = None
units_after_sensitivity = None
else:
total_sensitivity = None
sensitivity_frequency = None
units_after_sensitivity = None
index = {
# Information.
"network":
network.code,
"network_name":
network.description,
"station":
station.code,
"station_name":
station.description
if station.description else station.site.name,
"location":
channel.location_code,
"channel":
channel.code,
# Coordinates and orientation.
"latitude":
channel.latitude,
"longitude":
channel.longitude,
"elevation_in_m":
channel.elevation,
"depth_in_m":
channel.depth,
"dip":
channel.dip,
"azimuth":
channel.azimuth,
# Dates.
"start_date":
str(channel.start_date),
"end_date":
str(channel.end_date)
if channel.end_date is not None else None,
# This is strictly speaking not channel level
# information but needed to for a fast generation of
# the station level fdsnws responses.
"station_creation_date":
str(station.creation_date)
if station.creation_date is not None else None,
# Characteristics.
"sample_rate":
float(channel.sample_rate),
"sensor_type":
channel.sensor.type if channel.sensor else None,
# Some things have to be extracted from the response.
"total_sensitivity":
total_sensitivity,
"sensitivity_frequency":
sensitivity_frequency,
"units_after_sensitivity":
units_after_sensitivity,
# Geometry for PostGIS.
"geometry":
[Point(channel.longitude, channel.latitude)],
}
try:
plt.close()
except:
pass
# Sometimes fails. Wrap in try/except.
try:
# Plot response.
with io.BytesIO() as plot:
channel.plot(min_freq=1E-3, outfile=plot)
plot.seek(0)
index["attachments"] = {
"response": {
"content-type": "image/png",
"data": plot.read()
}
}
except Exception:
pass
finally:
try:
plt.close()
except:
pass
indices.append(index)
return indices
pylab.xlabel("Data as of " + lastdate)
pylab.title('Security Space Survey of\nPublic Subversion DAV Servers')
# End drawing
###########################################################
png = open(OUTPUT_FILE, 'w')
pylab.savefig(png)
png.close()
os.rename(OUTPUT_FILE, OUTPUT_FILE + ".tmp.png")
try:
im = Image.open(OUTPUT_FILE + ".tmp.png", 'r')
(width, height) = im.size
print("Original size: %d x %d pixels" % (width, height))
scale = float(OUTPUT_IMAGE_WIDTH) / float(width)
width = OUTPUT_IMAGE_WIDTH
height = int(float(height) * scale)
print("Final size: %d x %d pixels" % (width, height))
im = im.resize((width, height), Image.ANTIALIAS)
im.save(OUTPUT_FILE, im.format)
os.unlink(OUTPUT_FILE + ".tmp.png")
except Exception, e:
sys.stderr.write("Error attempting to resize the graphic: %s\n" % (str(e)))
os.rename(OUTPUT_FILE + ".tmp.png", OUTPUT_FILE)
raise
pylab.close()
if __name__ == '__main__':
dates, counts = load_stats()
draw_graph(dates, counts)
print("Don't forget to update ../../www/svn-dav-securityspace-survey.html!")
def plot_options_greedy(self, sess, coord, saver):
eigenvectors_path = os.path.join(
os.path.join(self.config.stage_logdir, "models"),
"eigenvectors.npy")
eigenvalues_path = os.path.join(
os.path.join(self.config.stage_logdir, "models"),
"eigenvalues.npy")
eigenvectors = np.load(eigenvectors_path)
eigenvalues = np.load(eigenvalues_path)
for k in ["poz", "neg"]:
for option in range(len(eigenvalues)):
# eigenvalue = eigenvalues[option]
eigenvector = eigenvectors[
option] if k == "poz" else -eigenvectors[option]
prefix = str(option) + '_' + k + "_"
plt.clf()
with sess.as_default(), sess.graph.as_default():
for idx in range(self.nb_states):
dx = 0
dy = 0
d = False
s, i, j = self.env.get_state(idx)
if not self.env.not_wall(i, j):
plt.gca().add_patch(
patches.Rectangle(
(j, self.config.input_size[0] - i -
1), # (x,y)
1.0, # width
1.0, # height
facecolor="gray"))
continue
# Image.fromarray(np.asarray(scipy.misc.imresize(s, [512, 512], interp='nearest'), np.uint8)).show()
feed_dict = {self.orig_net.observation: np.stack([s])}
fi = sess.run(self.orig_net.fi, feed_dict=feed_dict)[0]
transitions = []
terminations = []
for a in range(self.action_size):
s1, r, d, _ = self.env.fake_step(a)
feed_dict = {
self.orig_net.observation: np.stack([s1])
}
fi1 = sess.run(self.orig_net.fi,
feed_dict=feed_dict)[0]
transitions.append(
self.cosine_similarity((fi1 - fi),
eigenvector))
terminations.append(d)
transitions.append(
self.cosine_similarity(np.zeros_like(fi),
eigenvector))
terminations.append(True)
a = np.argmax(transitions)
# if a == 4:
# d = True
if a == 0: # up
dy = 0.35
elif a == 1: # right
dx = 0.35
elif a == 2: # down
dy = -0.35
elif a == 3: # left
dx = -0.35
if terminations[a] or np.all(
transitions[a] == np.zeros_like(
fi)): # termination
circle = plt.Circle(
(j + 0.5,
self.config.input_size[0] - i + 0.5 - 1),
0.025,
color='k')
plt.gca().add_artist(circle)
continue
plt.arrow(j + 0.5,
self.config.input_size[0] - i + 0.5 - 1,
dx,
dy,
head_width=0.05,
head_length=0.05,
fc='k',
ec='k')
plt.xlim([0, self.config.input_size[1]])
plt.ylim([0, self.config.input_size[0]])
for i in range(self.config.input_size[1]):
plt.axvline(i, color='k', linestyle=':')
plt.axvline(self.config.input_size[1],
color='k',
linestyle=':')
for j in range(self.config.input_size[0]):
plt.axhline(j, color='k', linestyle=':')
plt.axhline(self.config.input_size[0],
color='k',
linestyle=':')
plt.savefig(
os.path.join(
self.summary_path,
"SuccessorFeatures_" + prefix + 'policy.png'))
plt.close()
def cov_plot(self, matrix, station="", hour="", date="", averaged=""):
""" Basic plot for the correlation matrix """
var = self.var_dics[self.var]['name']
fig, ax = plt.subplots()
date = self.date_prettyfier(date)
hour = str(hour).replace('0', '00:00').replace('1', '12:00')
if not averaged:
title = "Stat: " + station + ', H: ' + hour + ', Date: ' + date + ', ' + var
filename = 'Cov_' + station + '_hour_' + hour.replace(
':', '') + '_date_' + str(date).replace('/', '') + '_' + var
elif averaged:
title = var.replace(
'temp', 'Temp.') + " , Stat: " + station + ', H: ' + str(
hour) + ', Date: ' + str(date)
filename = 'Cov_' + station + '_hour_' + str(hour).replace(
':', '') + '_averaged_' + str(date).replace('/',
'') + '_' + var
plt.title(title.replace('_', ' '), y=1.03, fontsize=self.font - 2)
num = len(matrix[0, :])
Num = range(num)
vmin, vmax = -3, 3
if self.var == 'direction':
vmin, vmax = -10, 10
color_map = plt.imshow(
matrix,
interpolation='nearest',
cmap='RdYlBu',
vmin=vmin,
vmax=vmax
) # nearest serves for discreete grid # cmaps blue, seismic
plt.ylim(-0.5, 15.5)
plt.xlim(-0.5, 15.5)
plt.xticks(Num, Num)
plt.xlabel('Pressure level an_dep [hPa]', fontsize=self.font - 2)
plt.yticks(Num, Num)
plt.ylabel('Pressure level fg_dep [hPa]', fontsize=self.font - 2)
ax.set_xticklabels(labels=self.pretty_pressure,
fontsize=self.font - 4,
rotation=45)
ax.set_yticklabels(labels=self.pretty_pressure, fontsize=self.font - 4)
bar = plt.colorbar()
bar.ax.set_ylabel("Covariance", fontsize=self.font)
for i in Num: # creating text labels
for j in Num:
value = '{0:.2f}'.format(matrix[i, j])
text = ax.text(j,
i,
value,
ha='center',
va='center',
color='black',
fontsize=5)
if not os.path.isdir('plots/covariances/' + station):
os.mkdir('plots/covariances/' + station)
plt.savefig('plots/covariances/' + station + '/' + filename + '.png',
bbox_inches='tight',
dpi=200)
plt.close()
def extract_data(files):
# find max test accuracy (i.e. test error convergence)
data = np.genfromtxt(files[0], delimiter=",")[1:]
# get max test index and value
max_test_idx = data.argmax(axis=0)[2]
with open("../Out/csv/5_max.csv", "w") as f:
f.write("epoch,train accuracy,test_accuracy\n")
entry = data[max_test_idx]
f.write("%s,%s,%s\n" % (entry[0], entry[1], entry[2]))
# process data
train_data = np.delete(data, [0, 2, 3], axis=1)
test_data = np.delete(data, [0, 1, 3], axis=1)
# plot to nearest hundreds
rounded_epoch = roundup_hundreds(max_test_idx)
fig, ax = plt.subplots(figsize=(16, 8))
ax.set_ylabel("Accuracy")
ax.set_xlabel("Epoch")
ax.plot(
range(rounded_epoch),
train_data[0:rounded_epoch],
label="Train Accuracy",
color="#0000FF",
)
ax.plot(
range(rounded_epoch),
test_data[0:rounded_epoch],
label="Test Accuracy",
color="#FF0000",
)
ax.legend()
fig.savefig("../Out/graph/5_epoch_" + str(rounded_epoch) + ".png")
plt.close()
# plot to max epoch
fig, ax = plt.subplots(figsize=(16, 8))
ax.set_ylabel("Accuracy")
ax.set_xlabel("Epoch")
ax.plot(range(epochs), train_data, label="Train Accuracy", color="#0000FF")
ax.plot(range(epochs), test_data, label="Test Accuracy", color="#FF0000")
ax.legend()
fig.savefig("../Out/graph/5_epoch_" + str(epochs) + ".png")
plt.close()
# plot to larger of 1 and 5 epoch
data_1 = np.genfromtxt(files[1], delimiter=",")[1:]
# process data 1
train_data_1 = np.delete(data_1, [0, 2, 3], axis=1)
test_data_1 = np.delete(data_1, [0, 1, 3], axis=1)
max_test_idx_1 = int(data_1.argmax(axis=0)[2])
with open("../Out/csv/4_optimal_max.csv", "w") as f:
f.write("epoch,train accuracy,test_accuracy\n")
entry = data_1[max_test_idx_1]
f.write("%s,%s,%s\n" % (entry[0], entry[1], entry[2]))
# find index of higher test accuracy convergence
if data[max_test_idx][2] <= data_1[max_test_idx_1][2]:
max_idx = max_test_idx_1
else:
max_idx = max_test_idx
rounded_epoch = roundup_hundreds(max_idx)
# plot train vs train
fig, ax = plt.subplots(figsize=(16, 8))
ax.set_ylabel("Accuracy")
ax.set_xlabel("Epoch")
ax.plot(
range(rounded_epoch),
train_data[0:rounded_epoch],
label="Train Accuracy (4-Layer)",
color="#0000FF",
)
ax.plot(
range(rounded_epoch),
train_data_1[0:rounded_epoch],
label="Train Accuracy (3-Layer)",
color="#FF0000",
)
ax.legend()
fig.savefig("../Out/graph/5_epoch_" + str(rounded_epoch) +
"_train_comparison.png")
plt.close()
# plot test vs test
fig, ax = plt.subplots(figsize=(16, 8))
ax.set_ylabel("Accuracy")
ax.set_xlabel("Epoch")
ax.plot(
range(rounded_epoch),
test_data[0:rounded_epoch],
label="Test Accuracy (4-Layer)",
color="#0000FF",
)
ax.plot(
range(rounded_epoch),
test_data_1[0:rounded_epoch],
label="Test Accuracy (3-Layer)",
color="#FF0000",
)
ax.legend()
fig.savefig("../Out/graph/5_epoch_" + str(rounded_epoch) +
"_test_comparison.png")
plt.close()
def plotTEx(job, tex, filterName, texSpecName='design', outputPrefix=''):
"""Plot TEx correlation function measurements and thresholds.
Parameters
----------
job : `lsst.verify.Job`
`Job` providing access to metrics, specs, and measurements
tex : `lsst.verify.Measurement
The ellipticity residual correlation `Measurement` object
filterName : str
Name of the filter of the images
texSpecName : str
Level of requirement to compare against.
Must be a into the metrics specified in the tex Measurement object
Typically one of 'design', 'minimum', 'stretch'
outputPrefix : str, optional
Prefix to use for filename of plot file.
Effects
-------
Saves an output plot file to that starts with specified outputPrefix.
"""
fig = plt.figure(figsize=(10, 6))
ax1 = fig.add_subplot(1, 1, 1)
# Plot correlation vs. radius
radius = tex.extras['radius'].quantity
xip = tex.extras['xip'].quantity
xip_err = tex.extras['xip_err'].quantity
D = tex.extras['D'].quantity
bin_range_operator = tex.extras['bin_range_operator'].quantity
ax1.errorbar(radius.value, xip.value, yerr=xip_err.value)
ax1.set_xscale('log')
ax1.set_xlabel('Separation (arcmin)', size=19)
ax1.set_ylabel('Median Residual Ellipticity Correlation', size=19)
# Overlay requirements level
metric_name = tex.metric_name
texSpec = job.specs[Name(package=metric_name.package,
metric=metric_name.metric,
spec=texSpecName)]
texSpecLabel = '{tex.datum.label} {specname}: {texSpec:.2g}'.format(
tex=tex, texSpec=texSpec.threshold, specname=texSpecName)
ax1.axhline(texSpec.threshold.value,
0,
1,
linewidth=2,
color='red',
label=texSpecLabel)
# Overlay measured KPM whether it passed or failed.
if texSpec.check(tex.quantity):
texStatus = 'passed'
else:
texStatus = 'failed'
texLabelTemplate = '{tex.datum.label} measured: {tex.quantity:.2g} ({status})'
texLabel = texLabelTemplate.format(tex=tex, status=texStatus)
ax1.axhline(tex.quantity.value,
0,
1,
linewidth=2,
color='black',
label=texLabel)
titleTemplate = """
{metric} Residual PSF Ellipticity Correlation
{bin_range_operator:s} {D.value:.1f}{D.unit:latex}
"""
title = titleTemplate.format(metric=tex.datum.label,
bin_range_operator=bin_range_operator,
D=D)
ax1.set_title(title)
ax1.set_xlim(0.0, 20.0)
ax1.set_xlabel('{radius.label} ({unit})'.format(
radius=tex.extras['radius'], unit=radius.unit._repr_latex_()))
ax1.set_ylabel('Correlation')
ax1.legend(loc='upper right', fontsize=16)
ext = 'png'
pathFormat = '{metric}_D_{D:d}_{Dunits}.{ext}'
plotPath = makeFilename(outputPrefix,
pathFormat,
metric=tex.datum.label,
D=int(D.value),
Dunits=D.unit,
ext=ext)
plt.tight_layout() # fix padding
plt.savefig(plotPath, dpi=300, ext=ext)
plt.close(fig)
print("Wrote plot:", plotPath)
def outliers_example(self,
corr='',
out='',
date='',
N='',
lower='',
upper='',
median='',
flag='',
upper_s='',
lower_s='',
station='',
what=''):
pressure = self.pretty_pressure_dic[str(self.an_p)]
var = self.var_dics[self.var]['name']
hour = str(self.hour).replace('0', '00:00').replace('1', '12:00')
plt.title(var + ' ' + what + ' Outliers - Stat: ' + station + ', H: ' +
hour + ', P: ' + pressure + ' [hPa]',
y=1.03)
corr_ = [n for n in corr if not np.isnan(n)]
out_ = [n for n in out if not np.isnan(n)]
num_a = '{:.1f}'.format(len(corr_) / len(out_ + corr_) * 100)
num_o = '{:.1f}'.format(len(out_) / len(out_ + corr_) * 100)
plt.scatter(date,
corr,
label='Accepted [' + num_a + '%]',
color='cyan',
s=3)
plt.scatter(date,
out,
label='Outliers [' + num_o + '%]',
color='black',
s=3)
X = [min(date), max(date)]
plt.plot(X, [lower, lower], label='Lower', color='blue', ls='--')
plt.plot(X, [upper, upper], label='Upper', color='red', ls='--')
# adding the upper and lower values for skewed distributions
plt.plot(X, [lower_s, lower_s],
label='Lower Skewed',
color='blue',
ls='-')
plt.plot(X, [upper_s, upper_s],
label='Upper Skewed',
color='red',
ls='-')
plt.plot(X, [median, median],
label='Median [' + '{:.1f}'.format(median) + ']',
color='black',
ls='--')
plt.legend(fontsize=self.font - 6, loc='upper right', ncol=2)
plt.grid(linestyle=':', color='lightgray', lw=1.2)
plt.ylabel('Departure ' + self.var_dics[self.var]['units'],
fontsize=self.font)
plt.xlabel('Date', fontsize=self.font)
plt.xticks(rotation=45)
out_c = [n for n in out if not np.isnan(n)]
corr_c = [n for n in corr if not np.isnan(n)]
plt.xlim(min(date) - 1 / 365, max(date) + 1 / 365)
plt.ylim(-10, 10)
plt.savefig('plots/outliers/outliers_' + flag + '_' + str(N) +
'_date_' + str(min(date)) + '_hour_' + self.hour + '_' +
self.var + '_anp_' + str(self.an_p) + '_fgp_' +
str(self.fg_p) + '.png',
bbox_inches='tight')
plt.close()
def plotPA1(pa1, outputPrefix=""):
"""Plot the results of calculating the LSST SRC requirement PA1.
Creates a file containing the plot with a filename beginning with
`outputPrefix`.
Parameters
----------
pa1 : `lsst.verify.Measurement`
A `Measurement` of the PA1 `Metric`.
outputPrefix : `str`, optional
Prefix to use for filename of plot file. Will also be used in plot
titles. E.g., outputPrefix='Cfht_output_r_' will result in a file
named ``'Cfht_output_r_AM1_D_5_arcmin_17.0-21.5.png'``
for an ``AMx.name=='AM1'`` and ``AMx.magRange==[17, 21.5]``.
"""
diffRange = (-100, +100)
magDiff = pa1.extras['magDiff'].quantity
magMean = pa1.extras['magMean'].quantity
rms = pa1.extras['rms'].quantity
iqr = pa1.extras['iqr'].quantity
fig = plt.figure(figsize=(18, 12))
ax1 = fig.add_subplot(1, 2, 1)
ax1.scatter(magMean[0],
magDiff[0],
s=10,
color=color['bright'],
linewidth=0)
# index 0 because we show only the first sample from multiple trials
ax1.axhline(+rms[0].value, color=color['rms'], linewidth=3)
ax1.axhline(-rms[0].value, color=color['rms'], linewidth=3)
ax1.axhline(+iqr[0].value, color=color['iqr'], linewidth=3)
ax1.axhline(-iqr[0].value, color=color['iqr'], linewidth=3)
ax2 = fig.add_subplot(1, 2, 2, sharey=ax1)
ax2.hist(magDiff[0],
bins=25,
range=diffRange,
orientation='horizontal',
histtype='stepfilled',
normed=True,
color=color['bright'])
ax2.set_xlabel("relative # / bin")
labelTemplate = r'PA1({label}) = {q.value:4.2f} {q.unit:latex}'
yv = np.linspace(diffRange[0], diffRange[1], 100)
ax2.plot(scipy.stats.norm.pdf(yv, scale=rms[0]),
yv,
marker='',
linestyle='-',
linewidth=3,
color=color['rms'],
label=labelTemplate.format(label='RMS', q=rms[0]))
ax2.plot(scipy.stats.norm.pdf(yv, scale=iqr[0]),
yv,
marker='',
linestyle='-',
linewidth=3,
color=color['iqr'],
label=labelTemplate.format(label='IQR', q=iqr[0]))
ax2.set_ylim(*diffRange)
ax2.legend()
ax1.set_xlabel("psf magnitude")
ax1.set_ylabel(r"psf magnitude diff ({0.unit:latex})".format(magDiff))
for label in ax2.get_yticklabels():
label.set_visible(False)
plt.tight_layout() # fix padding
ext = 'png'
pathFormat = "{name}.{ext}"
plotPath = makeFilename(outputPrefix, pathFormat, name="PA1", ext=ext)
plt.savefig(plotPath, format=ext)
plt.close(fig)
print("Wrote plot:", plotPath)
def plotAstrometryErrorModel(dataset, astromModel, outputPrefix=''):
"""Plot angular distance between matched sources from different exposures.
Creates a file containing the plot with a filename beginning with
`outputPrefix`.
Parameters
----------
dataset : `lsst.verify.Blob`
Blob with the multi-visit photometry model.
photomModel : `lsst.verify.Blob`
A `Blob` containing the analytic photometry model.
outputPrefix : str, optional
Prefix to use for filename of plot file. Will also be used in plot
titles. E.g., ``outputPrefix='Cfht_output_r_'`` will result in a file
named ``'Cfht_output_r_check_astrometry.png'``.
"""
bright, = np.where(
dataset['snr'].quantity > astromModel['brightSnr'].quantity)
dist = dataset['dist'].quantity
numMatched = len(dist)
dist_median = np.median(dist)
bright_dist_median = np.median(dist[bright])
fig, ax = plt.subplots(ncols=2, nrows=1, figsize=(18, 12))
ax[0].hist(dist,
bins=100,
color=color['all'],
histtype='stepfilled',
orientation='horizontal')
ax[0].hist(dist[bright],
bins=100,
color=color['bright'],
histtype='stepfilled',
orientation='horizontal')
ax[0].set_ylim([0., 500.])
ax[0].set_ylabel("Distance [{unit:latex}]".format(unit=dist.unit))
plotOutlinedAxline(
ax[0].axhline,
dist_median.value,
color=color['all'],
label="Median RMS: {v.value:.1f} {v.unit:latex}".format(v=dist_median))
plotOutlinedAxline(
ax[0].axhline,
bright_dist_median.value,
color=color['bright'],
label="SNR > {snr:.0f}\nMedian RMS: {v.value:.1f} {v.unit:latex}".
format(snr=astromModel['brightSnr'].quantity.value,
v=bright_dist_median))
ax[0].legend(loc='upper right')
snr = dataset['snr'].quantity
ax[1].scatter(snr, dist, s=10, color=color['all'], label='All')
ax[1].scatter(snr[bright],
dist[bright],
s=10,
color=color['bright'],
label='SNR > {0:.0f}'.format(
astromModel['brightSnr'].quantity.value))
ax[1].set_xlabel("SNR")
ax[1].set_xscale("log")
ax[1].set_ylim([0., 500.])
matchCountTemplate = '\n'.join(
['Matches:', '{nBright:d} high SNR,', '{nAll:d} total'])
ax[1].text(0.6,
0.6,
matchCountTemplate.format(nBright=len(bright), nAll=numMatched),
transform=ax[1].transAxes,
ha='left',
va='baseline')
w, = np.where(dist < 200 * u.marcsec)
plotAstromErrModelFit(snr[w], dist[w], astromModel, ax=ax[1])
ax[1].legend(loc='upper right')
ax[1].axvline(astromModel['brightSnr'].quantity,
color='red',
linewidth=4,
linestyle='dashed')
plotOutlinedAxline(ax[0].axhline, dist_median.value, color=color['all'])
plotOutlinedAxline(ax[0].axhline,
bright_dist_median.value,
color=color['bright'])
# Using title rather than suptitle because I can't get the top padding
plt.suptitle("Astrometry Check : %s" % outputPrefix, fontsize=30)
ext = 'png'
pathFormat = "{name}.{ext}"
plotPath = makeFilename(outputPrefix,
pathFormat,
name="check_astrometry",
ext=ext)
plt.savefig(plotPath, format=ext)
plt.close(fig)
print("Wrote plot:", plotPath)
def plotPhotometryErrorModel(dataset,
photomModel,
filterName='',
outputPrefix=''):
"""Plot photometric RMS for matched sources.
Parameters
----------
dataset : `lsst.verify.Blob`
A `Blob` with the multi-visit photometry model.
photomModel : `lsst.verify.Blob`
A `Blob` hlding the analytic photometry model parameters.
filterName : str, optional
Name of the observed filter to use on axis labels.
outputPrefix : str, optional
Prefix to use for filename of plot file. Will also be used in plot
titles. E.g., ``outputPrefix='Cfht_output_r_'`` will result in a file
named ``'Cfht_output_r_check_photometry.png'``.
"""
bright, = np.where(
dataset['snr'].quantity > photomModel['brightSnr'].quantity)
numMatched = len(dataset['mag'].quantity)
magrms = dataset['magrms'].quantity
mmagRms = magrms.to(u.mmag)
mmagRmsHighSnr = mmagRms[bright]
magerr = dataset['magerr'].quantity
mmagErr = magerr.to(u.mmag)
mmagErrHighSnr = mmagErr[bright]
mmagrms_median = np.median(mmagRms)
bright_mmagrms_median = np.median(mmagRmsHighSnr)
fig, ax = plt.subplots(ncols=2, nrows=2, figsize=(18, 16))
ax[0][0].hist(mmagRms,
bins=100,
range=(0, 500),
color=color['all'],
histtype='stepfilled',
orientation='horizontal')
ax[0][0].hist(mmagRmsHighSnr,
bins=100,
range=(0, 500),
color=color['bright'],
histtype='stepfilled',
orientation='horizontal')
plotOutlinedAxline(ax[0][0].axhline,
mmagrms_median.value,
color=color['all'],
label="Median RMS: {v:.1f}".format(v=mmagrms_median))
plotOutlinedAxline(ax[0][0].axhline,
bright_mmagrms_median.value,
color=color['bright'],
label="SNR > {snr:.0f}\nMedian RMS: {v:.1f}".format(
snr=photomModel['brightSnr'].quantity.value,
v=bright_mmagrms_median))
ax[0][0].set_ylim([0, 500])
ax[0][0].set_ylabel("{magrms.label} [{mmagrms.unit:latex}]".format(
magrms=dataset['magrms'], mmagrms=mmagRms))
ax[0][0].legend(loc='upper right')
mag = dataset['mag'].quantity
ax[0][1].scatter(mag, mmagRms, s=10, color=color['all'], label='All')
ax[0][1].scatter(mag[bright],
mmagRmsHighSnr,
s=10,
color=color['bright'],
label='{label} > {value:.0f}'.format(
label=photomModel['brightSnr'].label,
value=photomModel['brightSnr'].quantity.value))
ax[0][1].set_xlabel("{label} [{unit:latex}]".format(label=filterName,
unit=mag.unit))
ax[0][1].set_ylabel("{label} [{unit:latex}]".format(
label=dataset['magrms'].label, unit=mmagRmsHighSnr.unit))
ax[0][1].set_xlim([17, 24])
ax[0][1].set_ylim([0, 500])
ax[0][1].legend(loc='upper left')
plotOutlinedAxline(ax[0][1].axhline,
mmagrms_median.value,
color=color['all'])
plotOutlinedAxline(ax[0][1].axhline,
bright_mmagrms_median.value,
color=color['bright'])
matchCountTemplate = '\n'.join(
['Matches:', '{nBright:d} high SNR,', '{nAll:d} total'])
ax[0][1].text(0.1,
0.6,
matchCountTemplate.format(nBright=len(bright),
nAll=numMatched),
transform=ax[0][1].transAxes,
ha='left',
va='top')
ax[1][0].scatter(mmagRms, mmagErr, s=10, color=color['all'], label=None)
ax[1][0].scatter(mmagRmsHighSnr,
mmagErrHighSnr,
s=10,
color=color['bright'],
label=None)
ax[1][0].set_xscale('log')
ax[1][0].set_yscale('log')
ax[1][0].plot([0, 1000], [0, 1000],
linestyle='--',
color='black',
linewidth=2)
ax[1][0].set_xlabel("{label} [{unit:latex}]".format(
label=dataset['magrms'].label, unit=mmagRms.unit))
ax[1][0].set_ylabel("Median Reported Magnitude Err [{unit:latex}]".format(
unit=mmagErr.unit))
brightSnrMag = 2.5 * np.log10(
1 + (1 / photomModel['brightSnr'].quantity.value)) * u.mag
label = r'$SNR > {snr:.0f} \equiv \sigma < {snrMag:0.1f}$'.format(
snr=photomModel['brightSnr'].quantity.value,
snrMag=brightSnrMag.to(u.mmag))
ax[1][0].axhline(brightSnrMag.to(u.mmag).value,
color='red',
linewidth=4,
linestyle='dashed',
label=label)
ax[1][0].set_xlim([1, 500])
ax[1][0].set_ylim([1, 500])
ax[1][0].legend(loc='upper center')
ax[1][1].scatter(mag, mmagErr, color=color['all'], label=None)
ax[1][1].set_yscale('log')
ax[1][1].scatter(np.asarray(mag)[bright],
mmagErrHighSnr,
s=10,
color=color['bright'],
label=None)
ax[1][1].set_xlabel("{name} [{unit:latex}]".format(name=filterName,
unit=mag.unit))
ax[1][1].set_ylabel("Median Reported Magnitude Err [{unit:latex}]".format(
unit=mmagErr.unit))
ax[1][1].set_xlim([17, 24])
ax[1][1].set_ylim([1, 500])
ax[1][1].axhline(brightSnrMag.to(u.mmag).value,
color='red',
linewidth=4,
linestyle='dashed',
label=None)
w, = np.where(mmagErr < 200. * u.mmag)
plotPhotErrModelFit(mag[w].to(u.mag).value,
magerr[w].to(u.mmag).value,
photomModel,
ax=ax[1][1])
ax[1][1].legend(loc='upper left')
plt.suptitle("Photometry Check : %s" % outputPrefix, fontsize=30)
ext = 'png'
pathFormat = "{name}.{ext}"
plotPath = makeFilename(outputPrefix,
pathFormat,
name="check_photometry",
ext=ext)
plt.savefig(plotPath, format=ext)
plt.close(fig)
print("Wrote plot:", plotPath)
def plotAMx(job, amx, afx, filterName, amxSpecName='design', outputPrefix=""):
"""Plot a histogram of the RMS in relative distance between pairs of
stars.
Creates a file containing the plot with a filename beginning with
`outputPrefix`.
Parameters
----------
job : `lsst.verify.Job`
`~lsst.verify.Job` providing access to metrics, specs and measurements
amx : `lsst.verify.Measurement`
afx : `lsst.verify.Measurement`
filterName : `str`
amxSpecName : `str`, optional
Name of the AMx specification to reference in the plot.
Default: ``'design'``.
outputPrefix : `str`, optional
Prefix to use for filename of plot file. Will also be used in plot
titles. E.g., ``outputPrefix='Cfht_output_r_'`` will result in a file
named ``'Cfht_output_r_AM1_D_5_arcmin_17.0-21.5.png'``
for an ``AMx.name=='AM1'`` and ``AMx.magRange==[17, 21.5]``.
"""
if np.isnan(amx.quantity):
print("Skipping %s -- no measurement" % str(amx.metric_name))
return
fig = plt.figure(figsize=(10, 6))
ax1 = fig.add_subplot(1, 1, 1)
histLabelTemplate = 'D: [{inner.value:.1f}{inner.unit:latex}-{outer.value:.1f}{outer.unit:latex}]\n'\
'Mag: [{magBright:.1f}-{magFaint:.1f}]'
annulus = amx.extras['annulus'].quantity
magRange = amx.extras['magRange'].quantity
ax1.hist(amx.extras['rmsDistMas'].quantity,
bins=25,
range=(0.0, 100.0),
histtype='stepfilled',
label=histLabelTemplate.format(inner=annulus[0],
outer=annulus[1],
magBright=magRange[0],
magFaint=magRange[1]))
metric_name = amx.metric_name
amxSpec = job.specs[Name(package=metric_name.package,
metric=metric_name.metric,
spec=amxSpecName)]
amxSpecLabelTemplate = '{amx.datum.label} {specname}: {amxSpec.threshold:.1f}'
amxSpecLabel = amxSpecLabelTemplate.format(amx=amx,
specname=amxSpecName,
amxSpec=amxSpec)
ax1.axvline(amxSpec.threshold.value,
0,
1,
linewidth=2,
color='red',
label=amxSpecLabel)
if amxSpec.check(amx.quantity):
amxStatus = 'passed'
else:
amxStatus = 'failed'
amxLabelTemplate = '{amx.datum.label} measured: {amx.quantity:.1f} ({status})'
amxLabel = amxLabelTemplate.format(amx=amx, status=amxStatus)
ax1.axvline(amxSpec.threshold.value,
0,
1,
linewidth=2,
color='black',
label=amxLabel)
afxSpec = job.specs[Name(package=afx.metric_name.package,
metric=afx.metric_name.metric,
spec='srd')]
if afxSpec.check(afx.quantity):
afxStatus = 'passed'
else:
afxStatus = 'failed'
afxLabelTemplate = '{afx.datum.label} {afxSpec.name}: {afxSpec.threshold}%\n' + \
'{afx.datum.label} measured: {afx.quantity:.1f}% ({status})'
afxLabel = afxLabelTemplate.format(afx=afx,
afxSpec=afxSpec,
status=afxStatus)
ax1.axvline((amx.quantity + afx.extras['ADx'].quantity).value,
0,
1,
linewidth=2,
color='green',
label=afxLabel)
title = '{metric} Astrometric Repeatability over {D.value:.0f}{D.unit:latex}'.format(
metric=amx.datum.label, D=amx.extras['D'].quantity)
ax1.set_title(title)
ax1.set_xlim(0.0, 100.0)
ax1.set_xlabel('{rmsDistMas.label} ({unit})'.format(
rmsDistMas=amx.extras['rmsDistMas'],
unit=amx.extras['rmsDistMas'].quantity.unit._repr_latex_()))
ax1.set_ylabel('# pairs / bin')
ax1.legend(loc='upper right', fontsize=16)
ext = 'png'
pathFormat = '{metric}_D_{D:d}_{Dunits}_' + \
'{magBright.value}_{magFaint.value}_{magFaint.unit}.{ext}'
plotPath = makeFilename(outputPrefix,
pathFormat,
metric=amx.datum.label,
D=int(amx.extras['D'].quantity.value),
Dunits=amx.extras['D'].quantity.unit,
magBright=magRange[0],
magFaint=magRange[1],
ext=ext)
plt.tight_layout() # fix padding
plt.savefig(plotPath, dpi=300, format=ext)
plt.close(fig)
print("Wrote plot:", plotPath)