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_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 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 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 display_grid(grid, **kwargs):
fig = plt.figure()
plt.axes().set_aspect('equal')
if kwargs.get('mark_core_cells', True):
core_cell_coords = grid._cell_nodes[1:-1, 1:-1]
cellx, celly = core_cell_coords[:, :, 0], core_cell_coords[:, :, 1]
plt.plot(cellx, celly, '-o', np.transpose(cellx), np.transpose(celly), '-o', color='red')
if kwargs.get('mark_boundary_cells', True):
boundary_cell_coords = grid._cell_nodes[0, :], \
grid._cell_nodes[-1, :], \
grid._cell_nodes[1:-1, 0], \
grid._cell_nodes[1:-1, -1]
for coords in boundary_cell_coords:
plt.plot(coords[:, 0], coords[:, 1], '-x', color='blue')
if kwargs.get('show', False):
plt.show()
f = BytesIO()
plt.savefig(f)
return f
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 plot_feat_hist(data_name_list, filename=None):
if len(data_name_list)>1:
assert filename is not None
pylab.figure(num=None, figsize=(8, 6))
num_rows = 1 + (len(data_name_list) - 1) / 2
num_cols = 1 if len(data_name_list) == 1 else 2
pylab.figure(figsize=(5 * num_cols, 4 * num_rows))
for i in range(num_rows):
for j in range(num_cols):
pylab.subplot(num_rows, num_cols, 1 + i * num_cols + j)
x, name = data_name_list[i * num_cols + j]
pylab.title(name)
pylab.xlabel('Value')
pylab.ylabel('Fraction')
# the histogram of the data
max_val = np.max(x)
if max_val <= 1.0:
bins = 50
elif max_val > 50:
bins = 50
else:
bins = max_val
n, bins, patches = pylab.hist(
x, bins=bins, normed=1, facecolor='blue', alpha=0.75)
pylab.grid(True)
if not filename:
filename = "feat_hist_%s.png" % name.replace(" ", "_")
pylab.savefig(os.path.join(CHART_DIR, filename), bbox_inches="tight")
def make_plot_mG_nH(mgrpArr_all, denArr_all, over_density2, fignamestr, ngrp=15):
fig = plt.figure(3)
plt.clf()
ax = fig.add_subplot(111)
idArr, bins = pTdf.group_by_prop(mgrpArr_all, ngrp=ngrp, takelog=True, fixed_interval=True)
ngrp = len(bins) - 1
bins = 10.**bins
f_nHArr = N.zeros(len(bins)-1)
rho_mean = cTdf.mean_hydrogen_numden_z(simI["zcol"])
for igrp in xrange(ngrp):
isame = N.where(idArr == igrp)[0]
print "ptcls in [%.2e]: %d" % (bins[igrp], len(isame))
if len(isame) > 0:
ihigh = N.where(denArr_all[isame, izcol] >= over_density2*rho_mean)[0]
f_nHArr[igrp] = 1.*len(ihigh)/(1.*len(isame))
print "x({:d}): {:}".format(len(bins[:-1]+bins[1:]), (bins[:-1]+bins[1:])/2.)
print "y({:d}): {:}".format(len(f_nHArr), f_nHArr)
ax.plot((bins[:-1]+bins[1:])/2., f_nHArr)
ax.set_xlabel(r"$M_h$")
ax.set_ylabel(r"$f_{n_H > %d \bar{n_H}}(%.1f)$" % (over_density2, simI["zcol"]))
ax.set_xscale("log")
ax.set_xlim(bins[0], bins[-1]); ax.set_ylim(0., 1.1)
#plt.setp(ax.get_xticklabels(), fontsize=fs["tc"])
#plt.setp(ax.get_yticklabels(), fontsize=fs["tc"])
figname = "mgrp-fnH_%s_ov%d_vr%d.%s" % (fignamestr[1], int(over_density2), simI["virial_radius"], figext)
plt.savefig(os.path.join(fignamestr[2], figname))
def make_corr1d_fig(dosave=False):
corr = make_corr_both_hemi()
lw=2; fs=16
pl.figure(1)#, figsize=(8, 7))
pl.clf()
pl.xlim(4,300)
pl.ylim(-400,+500)
lambda_titles = [r'$20 < \lambda < 30$',
r'$30 < \lambda < 40$',
r'$\lambda > 40$']
colors = ['blue','green','red']
for i in range(3):
corr1d, rcen = corr_1d_from_2d(corr[i])
ipdb.set_trace()
pl.semilogx(rcen, corr1d*rcen**2, lw=lw, color=colors[i])
#pl.semilogx(rcen, corr1d*rcen**2, 'o', lw=lw, color=colors[i])
pl.xlabel(r'$s (Mpc)$',fontsize=fs)
pl.ylabel(r'$s^2 \xi_0(s)$', fontsize=fs)
pl.legend(lambda_titles, 'lower left', fontsize=fs+3)
pl.plot([.1,10000],[0,0],'k--')
s_bao = 149.28
pl.plot([s_bao, s_bao],[-9e9,+9e9],'k--')
pl.text(s_bao*1.03, 420, 'BAO scale')
pl.text(s_bao*1.03, 370, '%0.1f Mpc'%s_bao)
if dosave: pl.savefig('xi1d_3bin.pdf')
def plot_values(self, TITLE, SAVE):
plot(self.list_of_densities, self.list_of_pressures)
title(TITLE)
xlabel("Densities")
ylabel("Pressure")
savefig(SAVE)
show()
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 PlotTurbulenceIllustr(a):
"""
Can generate the grid with
g=kolmogorovutils.GenerateKolmogorov3D( 1025, 129, 129)
a=kolmogorovutils.GridToNumarray(g)
"""
for x in [1,10,100]:
suba= numarray.sum(a[:,:,0:x], axis=2)
suba.transpose()
pylab.clf()
pylab.matshow(suba)
pylab.savefig("temp/turb3d-sum%03i.eps" % x)
for x in [1,10,100]:
for j in [0,1,2]:
suba= numarray.sum(a[:,:200,j*x:(j+1)*x], axis=2)
suba.transpose()
pylab.clf()
pylab.matshow(suba)
pylab.savefig("temp/turb3d-sum%03i-s%i.eps" % (x,j))
def Animate(g):
for i in range(1,64,5):
pylab.clf()
x= g[0:i,:,:]
y= numarray.sum(x, axis=0)
pylab.matshow( y)
pylab.savefig("temp/3dturb-%03i.png" % i)
def visualization2(self, sp_to_vis=None):
if sp_to_vis:
species_ready = list(set(sp_to_vis).intersection(self.all_sp_signatures.keys()))
else:
raise Exception('list of driver species must be defined')
if not species_ready:
raise Exception('None of the input species is a driver')
for sp in species_ready:
# Setting up figure
plt.figure()
plt.subplot(313)
mon_val = OrderedDict()
signature = self.all_sp_signatures[sp]
for idx, mon in enumerate(list(set(signature))):
if mon[0] == 'C':
mon_val[self.all_comb[sp][mon] + (-1,)] = idx
else:
mon_val[self.all_comb[sp][mon]] = idx
mon_rep = [0] * len(signature)
for i, m in enumerate(signature):
if m[0] == 'C':
mon_rep[i] = mon_val[self.all_comb[sp][m] + (-1,)]
else:
mon_rep[i] = mon_val[self.all_comb[sp][m]]
# mon_rep = [mon_val[self.all_comb[sp][m]] for m in signature]
y_pos = numpy.arange(len(mon_val.keys()))
plt.scatter(self.tspan[1:], mon_rep)
plt.yticks(y_pos, mon_val.keys())
plt.ylabel('Monomials', fontsize=16)
plt.xlabel('Time(s)', fontsize=16)
plt.xlim(0, self.tspan[-1])
plt.ylim(0, max(y_pos))
plt.subplot(312)
for name in self.model.odes[sp].as_coefficients_dict():
mon = name
mon = mon.subs(self.param_values)
var_to_study = [atom for atom in mon.atoms(sympy.Symbol)]
arg_f1 = [numpy.maximum(self.mach_eps, self.y[str(va)][1:]) for va in var_to_study]
f1 = sympy.lambdify(var_to_study, mon)
mon_values = f1(*arg_f1)
mon_name = str(name).partition('__')[2]
plt.plot(self.tspan[1:], mon_values, label=mon_name)
plt.ylabel('Rate(m/sec)', fontsize=16)
plt.legend(bbox_to_anchor=(-0.1, 0.85), loc='upper right', ncol=1)
plt.subplot(311)
plt.plot(self.tspan[1:], self.y['__s%d' % sp][1:], label=parse_name(self.model.species[sp]))
plt.ylabel('Molecules', fontsize=16)
plt.legend(bbox_to_anchor=(-0.15, 0.85), loc='upper right', ncol=1)
plt.suptitle('Tropicalization' + ' ' + str(self.model.species[sp]))
# plt.show()
plt.savefig('s%d' % sp + '.png', bbox_inches='tight', dpi=400)
def test_flux(self):
tol = 150.
inputcat = catalog.read(os.path.join(self.args.tmp_path, 'ccd_1.cat'))
pixradius = 3*self.target["psf"]/self.instrument["PIXEL_SCALE"]
positions = list(zip(inputcat["X_IMAGE"]-1, inputcat["Y_IMAGE"]-1))
fluxes = image.simple_aper_phot(self.im[1], positions, pixradius)
sky_background = image.annulus_photometry(self.im[1], positions,
pixradius+5, pixradius+8)
total_bg_pixels = np.shape(image.build_annulus_mask(pixradius+5, pixradius+8, positions[0]))[1]
total_source_pixels = np.shape(image.build_circle_mask(pixradius,
positions[0]))[1]
estimated_fluxes = fluxes - sky_background*1./total_bg_pixels*total_source_pixels
estimated_magnitude = image.flux2mag(estimated_fluxes,
self.im[1].header['SIMMAGZP'], self.target["exptime"])
expected_flux = image.mag2adu(17.5, self.target["zeropoint"][0],
exptime=self.target["exptime"])
p.figure()
p.hist(fluxes, bins=50)
p.title('Expected flux: {:0.2f}, mean flux: {:1.2f}'.format(expected_flux, np.mean(estimated_fluxes)))
p.savefig(os.path.join(self.figdir,'Fluxes.png'))
assert np.all(np.abs(fluxes-expected_flux) < tol)
def plot_feat_hist(data_name_list, filename=None):
pylab.clf()
# import pdb;pdb.set_trace()
num_rows = 1 + (len(data_name_list) - 1) / 2
num_cols = 1 if len(data_name_list) == 1 else 2
pylab.figure(figsize=(5 * num_cols, 4 * num_rows))
for i in range(num_rows):
for j in range(num_cols):
pylab.subplot(num_rows, num_cols, 1 + i * num_cols + j)
x, name = data_name_list[i * num_cols + j]
pylab.title(name)
pylab.xlabel('Value')
pylab.ylabel('Density')
# the histogram of the data
max_val = np.max(x)
if max_val <= 1.0:
bins = 50
elif max_val > 50:
bins = 50
else:
bins = max_val
n, bins, patches = pylab.hist(
x, bins=bins, normed=1, facecolor='green', alpha=0.75)
pylab.grid(True)
if not filename:
filename = "feat_hist_%s.png" % name
pylab.savefig(os.path.join(CHART_DIR, filename), bbox_inches="tight")
def plotHist(outBaseStr,outData,motifID):
"""Plot histograms for each motif results."""
def _chooseBins():
"""Uses one of a number of heuristics to
choose the bins for each hist.
More discussed here:
http://en.wikipedia.org/wiki/Histogram#Number_of_bins_and_width"""
# sqrtChoice
# k = int(sqrt(n))+1
return int(math.sqrt(len(ctrls)))*3
outFile = '%s_%s_hist.pdf' % (outBaseStr,motifID)
ctrls = [x for x in outData[motifID][1:]]
yLab = 'Controls [n=%s]' % (len(ctrls))
xLab = 'Enrichment [p-value]'
fig = pl.figure()
ax = fig.add_subplot(111)
ax.set_ylabel(yLab)
ax.set_xlabel(xLab)
ax.set_xscale('log')
bins = _chooseBins()
hData = ax.hist(ctrls, bins=bins,histtype='stepfilled',color='grey',cumulative=1)
ax.axvline(x=outData[motifID][0] ,linewidth=2, color='r')
pl.savefig(outFile)
def show_CMB_T_map(self,Tmap=None, max=100, title = "CMB graviational potential fluctuations as seen from inside the LSS", from_perspective_of = "observer", cmap=None):
if Tmap is None:
self.NSIDE = 256
self.Tmap = hp.alm2map(self.alm,self.NSIDE)
else:
self.Tmap = Tmap
if from_perspective_of == "observer":
dpi = 300
figsize_inch = 60, 40
fig = plt.figure(figsize=figsize_inch, dpi=dpi)
# Sky map:
hp.mollview(self.Tmap, rot=(-90,0,0), min=-max, max=max, title=title + ", $\ell_{max}=$%d " % self.truncated_lmax, cmap=cmap, unit="$\mu$K")
plt.savefig(title+".png", dpi=dpi, bbox_inches="tight")
else:
# Interactive "external" view ([like this](http://zonca.github.io/2013/03/interactive-3d-plot-of-sky-map.html)) pass
# beatbox.zoncaview(self.Tmap)
# This did not work, sadly. Maybe we can find a 3D
# spherical surface plot routine using matplotlib? For
# now, just use the healpix vis.
R = (0.0,0.0,0.0) # (lon,lat,psi) to specify center of map and rotation to apply
hp.orthview(self.Tmap,rot=R,flip='geo',half_sky=True,title="CMB graviational potential fluctuations as seen from outside the LSS, $\ell_{max}$=%d" % self.truncated_lmax)
print "Ahem - we can't visualize maps on the surface of the sphere yet, sorry."
return
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 handle(self, *args, **options):
try:
from matplotlib import pylab as pl
import numpy as np
except ImportError:
raise Exception('Be sure to install requirements_scipy.txt before running this.')
all_names_and_counts = RawCommitteeTransactions.objects.all().values('attest_by_name').annotate(total=Count('attest_by_name')).order_by('-total')
all_names_and_counts_as_tuple_and_sorted = sorted([(row['attest_by_name'], row['total']) for row in all_names_and_counts], key=lambda row: row[1])
print "top ten attestors: (name, number of transactions they attest for)"
for row in all_names_and_counts_as_tuple_and_sorted[-10:]:
print row
n_bins = 100
filename = 'attestor_participation_distribution.png'
x_max = all_names_and_counts_as_tuple_and_sorted[-31][1] # eliminate top outliers from hist
x_min = all_names_and_counts_as_tuple_and_sorted[0][1]
counts = [row['total'] for row in all_names_and_counts]
pl.figure(1, figsize=(18, 6))
pl.hist(counts, bins=np.arange(x_min, x_max, (float(x_max)-x_min)/100) )
pl.title('Histogram of Attestor Participation in RawCommitteeTransactions')
pl.xlabel('Number of transactions a person attested for')
pl.ylabel('Number of people')
pl.savefig(filename)
def _fig_density(sweight, surweight, pval, nlm):
"""
Plot the histogram of sweight across the image
and the thresholds implied by the surrogate model (surweight)
"""
import matplotlib.pylab as mp
# compute some thresholds
nlm = nlm.astype('d')
srweight = np.sum(surweight,1)
srw = np.sort(srweight)
nitem = np.size(srweight)
thf = srw[int((1-min(pval,1))*nitem)]
mnlm = max(1,nlm.mean())
imin = min(nitem-1,int((1.-pval/mnlm)*nitem))
thcf = srw[imin]
h,c = np.histogram(sweight,100)
I = h.sum()*(c[1]-c[0])
h = h/I
h0,c0 = np.histogram(srweight,100)
I0 = h0.sum()*(c0[1]-c0[0])
h0 = h0/I0
mp.figure(1)
mp.plot(c,h)
mp.plot(c0,h0)
mp.legend(('true histogram','surrogate histogram'))
mp.plot([thf,thf],[0,0.8*h0.max()])
mp.text(thf,0.8*h0.max(),'p<0.2, uncorrected')
mp.plot([thcf,thcf],[0,0.5*h0.max()])
mp.text(thcf,0.5*h0.max(),'p<0.05, corrected')
mp.savefig('/tmp/histo_density.eps')
mp.show()
def plotFeaturePDF(ift, pft, outbase, fmin=0.0, fmax=1.0, fstep=0.01):
"""
Plot a comparison between the input feature distribution and the
feature distribution of the predicted halos
"""
plt.clf()
nfbins = ( fmax - fmin ) / fstep
fbins = np.logspace( fmin, fmax, nfbins )
fcen = ( fbins[:-1] + fbins[1:] ) / 2
plt.xscale( 'log', nonposx='clip' )
plt.yscale( 'log', nonposy='clip' )
ic, e, p = plt.hist( ift, fbins, label='Original Halos', alpha=0.5, normed=True )
pc, e, p = plt.hist( pft, fbins, label='Added Halos', alpha=0.5, normed=True )
plt.legend()
plt.xlabel( r'$\delta$' )
plt.savefig( outbase+'_fpdf.png' )
fdtype = np.dtype( [ ('fcen', float), ('ifcounts', float), ('pfcounts', float) ] )
fd = np.ndarray( len(fcen), dtype = fdtype )
fd[ 'mcen' ] = fcen
fd[ 'imcounts' ] = ic
fd[ 'pmcounts' ] = pc
fitsio.write( outbase+'_fpdf.fit', fd )
def plot_part2(filename):
"""
Plots the result of count ones test
"""
fig1 = pl.figure()
iterations, runtimes, fvals = extract(filename)
algos = ["SA", "GA", "MIMIC"]
iters_sa, iters_ga, iters_mimic = [np.array(iterations[a]) for a in algos]
runtime_sa, runtime_ga, runtime_mimic = [np.array(runtimes[a]) for a in algos]
fvals_sa, fvals_ga, fvals_mimic = [np.array(fvals[a]) for a in algos]
plotfunc = getattr(pl, "loglog")
plotfunc(runtime_sa, fvals_sa, "bs", mew=0)
plotfunc(runtime_ga, fvals_ga, "gs", mew=0)
plotfunc(runtime_mimic, fvals_mimic, "rs", mew=0)
# plotfunc(iters_sa, fvals_sa/(runtime_sa * iters_sa), "bs", mew=0)
# plotfunc(iters_ga, fvals_ga/(runtime_ga * iters_ga), "gs", mew=0)
# plotfunc(iters_mimic, fvals_mimic/(runtime_mimic * iters_mimic), "rs", mew=0)
pl.xlabel("Runtime (seconds)")
pl.ylabel("Objective function value")
pl.ylim([min(fvals_sa) / 2, max(fvals_mimic) * 2])
pl.legend(["SA", "GA", "MIMIC"], loc=4)
pl.savefig(filename.replace(".csv", ".png"), bbox_inches="tight")
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 plot_knowledge_count(agent_network, filename):
word_dict = dict()
agent_list = agent_network.get_all_agents()
for agent_item in agent_list:
for word in agent_item.knowledge:
if word not in word_dict:
word_dict[word] = 0
word_dict[word] = word_dict[word] + 1
word_count_tuple_list = word_dict.items()
word_count_tuple_list = sorted(word_count_tuple_list, key=itemgetter(1))
print word_count_tuple_list
x = list()
y = list()
for item in word_count_tuple_list:
word = item[0]
count = item[1]
x.append(word)
y.append(count)
plt.scatter(x, y, s=30, vmin = 0, vmax= 100, alpha=0.5)
plt.savefig(filename)
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 plotMassFunction(im, pm, outbase, mmin=9, mmax=13, mstep=0.05):
"""
Make a comparison plot between the input mass function and the
predicted projected correlation function
"""
plt.clf()
nmbins = ( mmax - mmin ) / mstep
mbins = np.logspace( mmin, mmax, nmbins )
mcen = ( mbins[:-1] + mbins[1:] ) /2
plt.xscale( 'log', nonposx = 'clip' )
plt.yscale( 'log', nonposy = 'clip' )
ic, e, p = plt.hist( im, mbins, label='Original Halos', alpha=0.5, normed = True)
pc, e, p = plt.hist( pm, mbins, label='Added Halos', alpha=0.5, normed = True)
plt.legend()
plt.xlabel( r'$M_{vir}$' )
plt.ylabel( r'$\frac{dN}{dM}$' )
#plt.tight_layout()
plt.savefig( outbase+'_mfcn.png' )
mdtype = np.dtype( [ ('mcen', float), ('imcounts', float), ('pmcounts', float) ] )
mf = np.ndarray( len(mcen), dtype = mdtype )
mf[ 'mcen' ] = mcen
mf[ 'imcounts' ] = ic
mf[ 'pmcounts' ] = pc
fitsio.write( outbase+'_mfcn.fit', mf )
def plot_bf_distributions():
# Bulge-fraction distribution
btf = genfromtxt('bt_distr_mstar.txt')
cmap = get_cmap('coolwarm')
labs = [
r"$9<\log\,M_\ast<9.25$", r"$9.25<\log\,M_\ast<9.5$",
r"$9.5<\log\,M_\ast<9.75$", r"$9.75<\log\,M_\ast<10$",
r"$10<\log\,M_\ast<10.25$", r"$10.25<\log\,M_\ast<10.5$",
r"$10.5<\log\,M_\ast<10.75$", r"$10.75<\log\,M_\ast<11$",
r"$\log\,M_\ast>11$"
]
fig = plt.figure()
ax = fig.add_subplot(111)
for i in range(2, 11):
c = linspace(0.01, 0.99, num=9)[i - 2]
ax.bar(btf[:, 0],
btf[:, i],
width=btf[:, 1] - btf[:, 0],
color='none',
edgecolor=cmap(c),
lw=3)
ax.text(0.35,
linspace(0.3, 0.7, num=9)[i - 2],
labs[i - 2],
fontsize=16,
color=cmap(c),
transform=ax.transAxes)
ax.axvline(0.2, ymin=0, ymax=1, ls='--', c='k')
ax.axvline(0.5, ymin=0, ymax=.26, ls='--', c='k')
ax.axvline(0.5, ymin=0.8, ymax=1, ls='--', c='k')
ax.axvline(0.8, ymin=0, ymax=1, ls='--', c='k')
ax.text(0.025,
0.9,
r"$\rm Sc-Sb$",
fontsize=18,
color='#151AB0',
transform=ax.transAxes)
ax.text(0.325,
0.9,
r"$\rm Sa$",
fontsize=18,
color='#008540',
transform=ax.transAxes)
ax.text(0.625,
0.9,
r"$\rm S0$",
fontsize=18,
color='#AB9700',
transform=ax.transAxes)
ax.text(0.875,
0.9,
r"$\rm Es$",
fontsize=18,
color='#BD000D',
transform=ax.transAxes)
ax.set_xlabel(r"$\rm B/T$", fontsize=18)
ax.set_ylabel(r"$\rm P(B/T)$", fontsize=18)
ax.set_xlim([0, 1])
plt.savefig("bt_hist_mstar.pdf", bbox_inches='tight')
plt.show()
def plot_results(filename, ccdnr=1, pngfile=None, panels='residual'):
#
#
#
if (not os.path.isfile(filename)):
raise FileNotFoundError
#
with fits.open(filename) as hdu:
resid = hdu['RESIDUALS'].data[ccdnr - 1, :, :]
errors = hdu['ERRORS'].data[ccdnr - 1, :, :]
chi2r = hdu['CHI2_R'].data[ccdnr - 1, :, :]
rev_start = hdu[0].header['REV0']
rev_end = hdu[0].header['REV1']
#
# calculate sigma_clipped statistics
#
xstat = stats.sigma_clipped_stats(resid, sigma=3, maxiters=3)
#
rawy_array = np.arange(20, 200, 20)
if (panels == 'all'):
fig, ax = plt.subplots(nrows=3, ncols=1, figsize=(10, 10), sharex=True)
im = ax[0].imshow(resid,
vmin=-100,
vmax=100.0,
origin='lower',
cmap=plt.get_cmap('bwr'))
div = make_axes_locatable(ax[0])
cax = div.append_axes("right", size="5%", pad=0.1)
cbar = plt.colorbar(im, cax=cax)
cbar.set_label('E - 8040 (eV)')
ax[0].set_title(f'CCD: {ccdnr}, revs in [{rev_start},{rev_end}]')
ax[0].set_xlabel(
fr'mean={xstat[0]:.1f} eV, st.dev.={xstat[2]:.1f} eV (3-$\sigma$ clipped)'
)
#ax[0].set_xticks(rawy_array)
#
im = ax[1].imshow(errors,
vmin=0.0,
vmax=20.0,
origin='lower',
cmap=plt.get_cmap('bwr'))
div = make_axes_locatable(ax[1])
cax = div.append_axes("right", size="5%", pad=0.1)
cbar = plt.colorbar(im, cax=cax)
cbar.set_label('Error (eV)')
#ax[1].set_title(f'CCD: {ccd}')
#ax[1].set_xticks(rawy_array)
#
im = ax[2].imshow(chi2r,
vmin=1.0,
vmax=2.0,
origin='lower',
cmap=plt.get_cmap('bwr'))
div = make_axes_locatable(ax[2])
cax = div.append_axes("right", size="5%", pad=0.1)
cbar = plt.colorbar(im, cax=cax)
cbar.set_label('Chi2_r')
#ax[2].set_title(f'CCD: {ccd}')
ax[2].set_xticks(rawy_array)
#
if (pngfile is not None):
plt.savefig(pngfile, dpi=100)
plt.show()
else:
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(10, 6), sharex=True)
im = ax.imshow(resid,
vmin=-100,
vmax=100.0,
origin='lower',
cmap=plt.get_cmap('bwr'))
div = make_axes_locatable(ax)
cax = div.append_axes("right", size="5%", pad=0.1)
cbar = plt.colorbar(im, cax=cax)
cbar.set_label('E - 8040 (eV)')
ax.set_xticks(rawy_array)
ax.set_xlabel('RAWY')
ax.set_ylabel('RAWX')
ax.set_title(
f'CCD: {ccdnr}, revs in [{rev_start},{rev_end}]\n' +
fr'mean={xstat[0]:.1f} eV, st.dev.={xstat[2]:.1f} eV (3-$\sigma$ clipped)'
)
#plt.title(fr'mean={xstat[0]:.1f} eV, st.dev.={xstat[2]:.1f} eV (3-$\sigma$ clipped)',ha='right',fontsize=16)
if (pngfile is not None):
plt.savefig(pngfile, dpi=100)
plt.show()
return
m = Basemap(llcrnrlon=-15.5,
llcrnrlat=-25.5,
urcrnrlon=15.5,
urcrnrlat=-4.5,
projection='merc',
resolution='l')
#Move to image directory
os.chdir(directory)
#Triplots for each file
print 'Making plots for %s...' % f
plt.figure('')
plt.clf()
cloud.five_plot(data='Nd')
fig = plt.gcf()
fig.set_size_inches(13.33, 7.5)
plt.savefig('%s_%s_%s_%s_Nd' % (year, month, day, cloud.time), dpi=150)
print 'Done!\n'
#
###Terra ACAERO
#
print 'Checking for new Terra ACAERO data...'
fdir = '/Users/michaeldiamond/Documents/oracles_files/terra/%s' % jday
os.chdir(fdir)
current_files = os.listdir(fdir)
new_files = []
path = 'allData/6/MOD06ACAERO/%s/%s/' % (year, jday)
files = []
#Try to access
ftp_worked = False
ax.set_ylim(0,8)
ax.tick_params(axis=u'both', which=u'both',length=0)
ax.set_xlabel('Measurement environment',fontsize=14)
ax.set_ylabel('Evolution environment',fontsize=14)
pt.plot([0,8],[8,0],'--',color='Gray',linewidth=.5)
for i in range(8):
for j in range(8):
if fitness_table[i,7-j] < 0 and fitness_table[i,7-j] > -.1: ###This will get printed as -0.0, so print 0.0 instead
ax.text(7-j+.5,7-i+.5,abs(numpy.round(fitness_table[i,7-j],1)),color='Gray',fontsize=7,horizontalalignment='center',verticalalignment='center')
elif i==7-j:
ax.text(7-j+.5,7-i+.5,numpy.round(fitness_table[i,7-j],1),color='k',fontsize=7,horizontalalignment='center',verticalalignment='center')
else:
ax.text(7-j+.5,7-i+.5,numpy.round(fitness_table[i,7-j],1),color='Gray',fontsize=7,horizontalalignment='center',verticalalignment='center')
pt.savefig('figures/median_fitness_heatmap_check.pdf',bbox_inches='tight')
##Plot the table with clones that lost the virus removed
pt.figure()
pt.pcolor( fitness_table_vplus[::-1], cmap = 'RdBu', vmin=-5,vmax=5,edgecolors='w' )
pt.colorbar(label='Median fitness (%)')
ax = pt.gca()
ax.set_xticks(numpy.arange(.5,8.7,1))
ax.set_yticks(numpy.arange(.5,8.7,1))
ax.set_xticklabels(evolution_env_labels,fontsize=8)
ax.set_yticklabels(measurement_env_labels[::-1],fontsize=8)
ax.set_xlim(0,8)
ax.set_ylim(0,8)
ax.tick_params(axis=u'both', which=u'both',length=0)
for word in model.vocab:
vocabulary.append(word)
vec.append(model[word])
vecLength = len(vec)
vec = np.array(vec)[:int((dataRatio * vecLength))]
vocabulary = vocabulary[:int((dataRatio * vecLength))]
tsne = TSNE(n_components=2, random_state=0)
yTransform = tsne.fit_transform(vec)
print("New Size: " + str(model.vectors.shape))
tags = set(['JJ', 'NNP', 'NN', 'NNS'])
puncts = ["'", ".", ":", ";", ",", "?", "!", u"’"]
plt.figure()
texts = []
nltk.download(
['averaged_perceptron_tagger', 'maxent_treebank_pos_tagger', 'punkt'])
for i, label in enumerate(vocabulary):
pos = nltk.pos_tag([label])
if (label[0].isupper() and len(label) > 1 and pos[0][1] in tags
and all(c not in label for c in puncts)):
x, y = yTransform[i, :]
texts.append(plt.text(x, y, label))
plt.scatter(x, y)
adjust_text(texts, arrowprops=dict(arrowstyle='-', color='k', lw=1.5))
plt.savefig('hp_result.png', dpi=600)
#plt.show()
#%%
# d_sim = percept_loss.forward(resz_ref_img, resz_out_img)
zcode, fitimg = img_backproj(target_img, percept_loss)
# zcode, fitimg = img_backproj(target_img, L1loss)
#%%
for nsteps in [1000]: #%150, 250, 500,
zcode, fitimg = img_backproj(target_img, percept_loss, nsteps=nsteps)
label = "alexPL_step%d" % (nsteps)
plt.figure(figsize=[4, 4.5])
plt.imshow(fitimg.cpu().numpy())
plt.title(label)
plt.axis("off")
plt.savefig(join(savedir, "Embed_%s.jpg" % label))
plt.show()
#%%
percept_net = models.PerceptualLoss(model='net-lin',
net='vgg',
use_gpu=1,
gpu_ids=[0])
def percept_loss(img, target, net=percept_net):
return net.forward(
img.unsqueeze(0).permute([0, 3, 1, 2]),
target.unsqueeze(0).permute([0, 3, 1, 2]))
from sklearn.naive_bayes import MultinomialNB
from os.path import join
# %pylab inline
plt.rcParams['text.usetex'] = True
pos = norm(loc=3, scale=2.5)
neg = norm(loc=-0.5, scale=0.75)
plt.clf()
for ins, color in zip([pos, neg], ['b', 'r']):
x = np.linspace(ins.ppf(0.001), ins.ppf(0.999))
plt.plot(x, ins.pdf(x), color)
plt.legend(['Positive', 'Negative'])
plt.grid()
plt.tight_layout()
plt.savefig('two_normals.png', dpi=300)
_min = neg.ppf(0.05)
_max = neg.ppf(0.95)
D = [(x, 0) for x in neg.rvs(100) if x >= _min and x <= _max]
D += [(x, 1) for x in pos.rvs(1000) if x < _min or x > _max]
plt.clf()
plt.plot([x for x, k in D if k == 1], pos.pdf([x for x, k in D if k == 1]),
'b.')
plt.plot([x for x, k in D if k == 0], neg.pdf([x for x, k in D if k == 0]),
'r.')
plt.grid()
plt.legend(['Positive', 'Negative'])
plt.tight_layout()
plt.savefig('two_normal_samples.png', dpi=300)
for stock in stocks:
print(stock)
dir_path = './result/%s' % stock
line = '頻度_rate, 日数, 高騰正解数, 高騰正答数, 下落正解数, 下落正答数, 高騰正答率(％), 下落正答率(％)\n'
for l in day_length_list:
with open('%s/result_%dd.csv' % (dir_path, l), 'r') as f:
lines = [line.strip() for line in f][1:]
actual_list = [float(line.split(',')[1]) for line in lines]
pred_list = [float(line.split(',')[2]) for line in lines]
plt.figure()
plt.title('stock_close/topix_close')
plt.plot(actual_list, label='actual')
plt.plot(pred_list, label='predict')
plt.legend()
filename = '%s/result_graph%dd.png' % (dir_path, l)
plt.savefig(filename)
values = [
(actual_list[idx] - actual_list[idx - l]) / actual_list[idx]
for idx in range(l, len(actual_list))
]
r_corrects = [1 if val > rate else 0 for val in values]
values = [(pred_list[idx] - pred_list[idx - l]) / pred_list[idx]
for idx in range(l, len(pred_list))]
prediction = [1 if val > rate else 0 for val in values]
# for idx in range(len(prediction)): print('%d, %d'%(r_corrects[idx], prediction[idx]))
raise_correct = sum(item for item in r_corrects)
count_raise = sum(1 if r_corrects[idx] == prediction[idx] else 0
for idx in range(len(prediction)))
values = [
(actual_list[idx] - actual_list[idx - l]) / actual_list[idx]
for idx in range(l, len(actual_list))
import numpy as np
import matplotlib.pylab as plt
Datos = np.genfromtxt("datos.dat", delimiter=";")
x = Datos[:, 0]
a = Datos[:, 1]
Datos2 = np.genfromtxt("datos2.dat", delimiter=";")
x2 = Datos2[:, 0]
a2 = Datos2[:, 1]
Datos3 = np.genfromtxt("datos3.dat", delimiter=";")
x3 = Datos3[:, 0]
a3 = Datos3[:, 1]
plt.figure()
plt.plot(x, a, label="Inicial", c="red")
plt.plot(x2, a2, label="arrAf", c="blue")
plt.plot(x3, a3, label="arrf", c="green")
plt.xlabel("X")
plt.ylabel("A")
plt.legend()
plt.savefig("ArevaloSergioS6C2.png")
def plot_angular_momentum_size_velocity():
size = 100000
# Planck parameters
h, Om, OL = 0.677, 0.31, 0.69
# uniform halo mass function
mhalo = array(10.**uniform(10.75, 14.5, size), dtype=float32)
# read halo mass-function
# mhf = genfromtxt('mVector_PLANCK-SMT_11-13.txt')
# mhf = genfromtxt('mVector_PLANCK-SMT_10.5-13.txt')
mhf = genfromtxt('mVector_PLANCK-SMT_11-14.5.txt')
# mhalo = array(choice(mhf[:, 0], p=mhf[:, 5]/sum(mhf[:, 5]), size=size), dtype=float32)
'''
Ms = Mstar(0., mode='low', model='B10')
mstar = []
print "generating mstar..."
for m in mhalo:
mstar.append(Ms(m))
mstar = array(mstar)
'''
mstar = Mstar_vU(mhalo, mode='TF')
ms_lowlim, ms_highlim = 7., 11.75
mhalo = mhalo[(log10(array(mstar)) > ms_lowlim)
& (log10(array(mstar)) < ms_highlim)]
mstar = mstar[(log10(array(mstar)) > ms_lowlim)
& (log10(array(mstar)) < ms_highlim)]
# DM halo spin parameter distribution
# from Maccio', Dutton & van den Bosch (2008)
lambda_halo = 10.**normal(-1.466, 0.253, len(mhalo))
# bt = get_bt_distribution_from_SDSS(mstar)
bt = get_bt_distribution_from_meert14(mstar)
# bt, mstar, mhalo, lambda_halo = get_bt_distribution_from_lambda(mstar, mhalo, lambda_halo)
# Dutton & Maccio' (2014)
# b = -0.101 + 0.026 * array([0., 1.])
# a = 0.52 + (0.905 - 0.52) * exp(-0.617 * array([0., 1.]) ** 1.21)
b = -0.097 + 0.024 * array([0., 1.])
a = 0.537 + (1.025 - 0.537) * exp(-0.718 * array([0., 1.])**1.08)
# scatter 0.11dex
cvir = []
print "generating concentrations..."
for m in mhalo:
cvir.append(10.**normal(a[0] + b[0] * log10(m / (1e12 / h)), 0.11,
1)[0])
cvir = array(cvir)
# Circular velocity for NFW haloes
G = 4.302e-3 * 1e-6 # Mpc Mo^-1 (km/s)^2
f = lambda x: log(1. + asarray(x)) - asarray(x) / (1. + asarray(x))
rho_c = 3. * (h * 100.)**2 / (8. * pi * G)
# Bryan & Norman (1998)
Oz = lambda z: Om * (1 + z)**3 / (Om * (1. + z)**3 + OL)
Delta_c = lambda z: 18. * pi**2 + 82. * (Oz(z) - 1.) - 39. * (Oz(z) - 1.
)**2
rho_hat = 4. / 3. * pi * Delta_c(0.) * rho_c
vc = sqrt(G * f(2.15) / f(cvir) * cvir / 2.15 *
pow(rho_hat, 1. / 3.)) * power(mhalo / h, 1. / 3.)
# print "%e %e" % (f(10.) * 2.15 / (f(2.15) * 10.), sqrt(2. * f(10.) * 2.15 / (f(2.15) * 10.)))
# Kravtsov 2013
# rho_200 = 4. / 3. * pi * 200. * rho_c
r200 = 1e3 * power(mhalo / rho_hat, 1. / 3.)
rs = []
for r in r200:
rs.append(10.**normal(log10(0.015 * r), 0.25, 1)[0])
rs = array(rs)
js = rs * vc
# jhalo - mhalo
fe = cvir / 2. * (1. - 1. / power(1. + cvir, 2) - 2. * log(1. + cvir) /
(1. + cvir)) / power(cvir /
(1. + cvir) - log(1. + cvir), 2)
# fe = f(2.15) / f(cvir) * cvir / 2.15
j_halo = sqrt(2. / fe) * lambda_halo * sqrt(G * 1e3 * mhalo / r200) * r200
# j_halo da Romanowsky & Fall (2012) eq. (14)
# j_halo = 4.23e4 * lambda_halo * power(mhalo / 1e12, 2./3.)
# bt_discs, bt_spirals, bt_ltg, bt_lents, bt_ells = 0.1, 0.2, 0.5, 0.8, 0.95
bt_discs, bt_spirals, bt_ltg, bt_lents, bt_ells = 0.2, 0.4, 0.5, 0.65, 0.8
# fj(Mhalo)
def jstar_FR(mass, bf):
if (bf >= 0.) & (bf <= bt_discs):
# Sc
j0, alpha, s = 3.29, 0.55, 0.18
elif (bf > bt_discs) & (bf <= bt_spirals):
# Sb
j0, alpha, s = 3.21, 0.68, 0.15
elif (bf > bt_spirals) & (bf <= bt_ltg):
# Sa
j0, alpha, s = 3.02, 0.64, 0.12
elif (bf > bt_ltg) & (bf <= bt_lents):
# S0
j0, alpha, s = 3.05, 0.8, 0.22
elif (bf > bt_lents) & (bf <= bt_ells):
# fE
j0, alpha, s = 2.875, 0.6, 0.2
elif (bf > bt_ells) & (bf <= 1.):
# sE
j0, alpha, s = 2.73, 0.6, 0.2
else:
print bf
raise ValueError("Problem in bt not in ]0,1]")
return 10.**normal(j0 + alpha * (mass - 11.), s, 1)[0]
# fitting function to jb/jd estimated from Romanowsky & Fall (2012) data
# jb/jd = 0.025 + B/T^2
# jd = j_star / (1 + (jb/jd-1)B/T)
# --> here jdisc = jstar / fb_func
jb_over_jd_fit = lambda fb: 0.025 + fb**2
fb_func = lambda fb: 1. + (jb_over_jd_fit(fb) - 1.) * fb
jstar, jdisc, jbulge = [], [], []
print "generating jstar..."
for i in range(len(mstar)):
jstar.append(jstar_FR(log10(mstar[i]), bt[i]))
jdisc.append(jstar[i] / fb_func(bt[i]))
jbulge.append(jdisc[i] * jb_over_jd_fit(bt[i]))
jstar, jdisc, jbulge = array(jstar), array(jdisc), array(jbulge)
fj = jstar / j_halo # jstar_FR(log10(0.158 * mhalo)) / j_halo
# Kravtsov
Mstar_TF = lambda t: 10.**(-0.61 + 4.93 * asarray(t)
) # McGaugh & Schombert (2015), sTF @ 3.6um
vstar_TF = lambda t: 10.**(0.61 / 4.93 + 1. / 4.93 * asarray(t))
sstar_FJ = lambda t: 10.**(2.054 + 0.286 * asarray(t - 10.))
Mstar_FJ = lambda t: 10.**(-2.054 / 0.286 + 10. + 1. / 0.286 * asarray(t))
# Re = jdisc / (vstar_TF(log10(mstar)))
# Re[bt > 0.8] = jbulge[bt > 0.8] / (0.7 * vstar_TF(log10(mstar[bt > 0.8])))
# Re[bt > 0.8] = jbulge[bt > 0.8] / (10.**(-1.06 + 0.32*log10(mstar[bt > 0.8])))
Re = jstar / vc # vstar_TF(log10(mstar))
# Re[bt > bt_ltg] = jstar[bt > bt_ltg] / (1.65 * sstar_FJ(log10(mstar[bt > bt_ltg])))
# Mo, Mao & White (1998)
# lambda_halo_prime = lambda_halo * jdisc / j_halo # fj
lambda_halo_prime = lambda_halo * fj # fj
cvir = array(cvir)
fac_sis_nfw = 1. / sqrt(
cvir / 2. * (1. - 1. / power(1. + cvir, 2) - 2. * log(1. + cvir) /
(1. + cvir)) / power(cvir /
(1. + cvir) - log(1. + cvir), 2))
# md = mstar / mhalo
# fac_sis_nfw *= pow(lambda_halo_prime / 0.1, -0.0 + 2.71 * md + 0.0047 / lambda_halo_prime) * \
# (1-3.*md+5.2*md*md) * (1-0.019*cvir * 0.00025*cvir*cvir + 0.52 / cvir)
Rd = 1. / sqrt(2.) * lambda_halo_prime * r200 * fac_sis_nfw
"""
HDF5 file output
"""
f = h5py.File("jstar-jhalo.hdf5", 'w')
group = f.create_group("columns")
dset_lambda = group.create_dataset("Lambda_Halo", data=lambda_halo)
dset_mhalo = group.create_dataset("Halo_Mass", data=mhalo)
dset_mstar = group.create_dataset("Galaxy_Mass", data=mstar)
dset_jhalo = group.create_dataset("Halo_Specific_Angular_Momentum",
data=j_halo)
dset_jstar = group.create_dataset("Galaxy_Specific_Angular_Momentum",
data=jstar)
dset_cvir = group.create_dataset("Halo_Concentration", data=cvir)
dset_fj = group.create_dataset("Retained_fraction_of_j", data=fj)
dset_bt = group.create_dataset("Bulge_Fraction", data=bt)
dset_vc = group.create_dataset("Circular_Velocity", data=vc)
dset_vc = group.create_dataset("Velocity_Dispersion", data=vc / 1.1)
dset_Re = group.create_dataset("Effective_Radius", data=Re)
dset_Rd = group.create_dataset("Disc_Scale_Radius", data=Rd)
"""
Plots
"""
# plt.plot(log10(mstar * bt), log10(jbulge), 'r.', alpha=0.005)
# plt.plot(log10(mstar * bt * (1./bt - 1.)), log10(jdisc), 'b.', alpha=0.005)
# plt.plot(linspace(9, 12), 3.28+0.67*(linspace(9, 12)-11.), 'k-', lw=3)
# plt.plot(linspace(9, 12), 2.75+0.67*(linspace(9, 12)-11.), 'k--', lw=3)
# plt.show()
size_hist = 20
sigs = [68., 90.]
save_plots = False
'''
----------- Mstar-Mhalo
'''
# Dutton et al. 2010 relations
d10_msmh_ltg = lambda x: 10.**1.61 * (asarray(x) / 10.**10.4)**-0.5 * (
0.5 + 0.5 * (asarray(x) / 10.**10.4))**0.5
d10_msmh_etg = lambda x: 10.**1.97 * (asarray(x) / 10.**10.8)**-0.15 * (
0.5 + 0.5 * (asarray(x) / 10.**10.8)**2)**0.5
d10_ms_ltg = logspace(9.35, 11)
d10_ms_etg = logspace(9.85, 11.4)
fig = plt.figure()
ax = fig.add_subplot(211)
ax.set_ylabel(r"$\log\rm\,M_\ast/M_\odot$", fontsize=16)
# ax.xlabel(r"$\log\rm\,M_h/M_\odot$", fontsize=16)
ax.axes.get_xaxis().set_visible(False)
ax.set_ylim([8, 11.75])
ax.set_xlim([10.75, 13.5])
x, y, H, lev, _, _, _ = bins_and_hist(mhalo, mstar, bt > 0, 30, sigs)
# plt.plot(log10(d10_msmh_ltg(d10_ms_ltg) * d10_ms_ltg), log10(d10_ms_ltg), 'b-')
# plt.plot(log10(d10_msmh_etg(d10_ms_etg) * d10_ms_etg), log10(d10_ms_etg), 'r-')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Greys'),
alpha=0.75)
plt.xlim()
ax2 = fig.add_subplot(212, sharex=ax)
ax2.set_ylabel(r"$\log\rm\,M_\ast/M_\odot$", fontsize=16)
ax2.set_xlabel(r"$\log\rm\,M_h/M_\odot$", fontsize=16)
ax2.set_xlim([10.75, 13.5])
fig.subplots_adjust(hspace=0)
x, y, H, lev, _, _, _ = bins_and_hist(mhalo, mstar / mhalo, bt > 0, 30,
sigs)
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Greys'),
alpha=0.75)
if save_plots:
plt.savefig('SHMR_all_ref.pdf', bbox_inches='tight')
'''
----------- lambda-Mhalo
'''
fig = plt.figure()
plt.xlabel(r"$\log\rm\,M_h/M_\odot$", fontsize=16)
plt.ylabel(r"$\log\rm\lambda_{halo}$", fontsize=16)
plt.plot(log10(mhalo), log10(lambda_halo), 'b.', alpha=0.0025)
x, y, H, lev, _, _, _ = bins_and_hist(mhalo, lambda_halo, bt > 0,
size_hist, sigs)
plt.contour(x, y, log10(H).T, levels=lev, colors='#151AB0')
'''
----------- j_halo - M_halo
'''
fig = plt.figure()
ax = fig.add_subplot(111)
plt.xlabel(r"$\log\rm\,M_h/M_\odot$", fontsize=16)
plt.ylabel(r"$\log\rm\,j_h/km\,s^{-1}\,kpc$", fontsize=16)
x, y, H, lev, _, _, _ = bins_and_hist(mhalo, j_halo, bt > 0, size_hist,
sigs)
# ax.contour(x, y, log10(H).T, levels=lev, colors='#151AB0')
ax.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Greys'),
alpha=0.75)
ax.plot(linspace(10.75, 13),
3.28 + 0.67 * (linspace(10.75, 13) - 11.),
'k--',
lw=3)
# plt.plot([12.5, log10(0.158 * 10.**12.5)], [3.505, 3.7481], 'm-', lw=3)
# ax.arrow(12.5, 3.505, -12.5+log10(0.08 * 10.**12.5), -3.505+3.28+0.67*(log10(0.08 * 10.**12.5)-11.)-0.045,
# head_width=0.075, head_length=0.05, fc='m', ec='m', lw=3)
ax.arrow(12.,
3.1704,
-12. + log10(0.08 * 10.**12.),
-3.1704 + 3.28 + 0.67 * (log10(0.08 * 10.**12.) - 11.) - 0.045,
head_width=0.075,
head_length=0.05,
fc='m',
ec='m',
lw=3)
ax.text(11.15,
4.,
r"$f_{\rm baryon}\simeq 0.16$" + "\n" + r"$M_\ast=M_{\rm bar}/2$",
color='m',
fontsize=18)
if save_plots:
plt.savefig('jh-Mh_all_ref.pdf', bbox_inches='tight')
'''
----------- fj(M_halo)
'''
fig = plt.figure()
plt.xlabel(r"$\log\rm\,M_h/M_\odot$", fontsize=16)
plt.ylabel(r"$\log\rm\,f_j(M_h)\equiv j_\ast / j_h$", fontsize=16)
ax = fig.add_subplot(111)
ax.text(0.1,
0.9,
r"$\rm Sc-Sb$",
fontsize=18,
color='#151AB0',
transform=ax.transAxes)
ax.text(0.1,
0.85,
r"$\rm Sa-S0$",
fontsize=18,
color='#009603',
transform=ax.transAxes)
ax.text(0.1,
0.8,
r"$\rm Es$",
fontsize=18,
color='#BD000D',
transform=ax.transAxes)
# spirals
w = bt < bt_spirals
# plt.plot(log10(mhalo[w]), log10(fj[w]), 'b.', alpha=0.0025)
x, y, H, lev, mhalo_bin, fj_bin, e_fj_bin = bins_and_hist(
mhalo, fj, w, size_hist, sigs)
# plt.errorbar(log10(mhalo_bin), log10(fj_bin), yerr=abs(log10(fj_bin)-log10(e_fj_bin)), c='b', fmt='o')
# plt.contour(x, y, log10(H).T, levels=lev, colors='#151AB0')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Blues'),
alpha=0.75)
# Sa and lenticulars
w = (bt >= bt_spirals) & (bt < bt_lents)
# plt.plot(log10(mhalo[w]), log10(fj[w]), 'b.', alpha=0.0025)
x, y, H, lev, mhalo_bin, fj_bin, e_fj_bin = bins_and_hist(
mhalo, fj, w, size_hist, sigs)
# plt.errorbar(log10(mhalo_bin), log10(fj_bin), yerr=abs(log10(fj_bin)-log10(e_fj_bin)), c='g', fmt='o')
# plt.contour(x, y, log10(H).T, levels=lev, colors='#AB9700')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Greens'),
alpha=0.75)
# ellipticals
w = bt > bt_lents
# plt.plot(log10(mhalo[w]), log10(fj[w]), 'r.', alpha=0.0025)
x, y, H, lev, mhalo_bin, fj_bin, e_fj_bin = bins_and_hist(
mhalo, fj, w, size_hist, sigs)
# plt.errorbar(log10(mhalo_bin), log10(fj_bin), yerr=abs(log10(fj_bin)-log10(e_fj_bin)), c='r', fmt='o')
# plt.contour(x, y, log10(H).T, levels=lev, colors='#BD000D')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Reds'),
alpha=0.75)
plt.xlim([10.7, 13.5])
# ------ Median relation
x, y, H, lev, mhalo_bin, fj_bin, e_fj_bin = bins_and_hist(mhalo,
fj,
bt > 0,
size_hist,
sigs,
bin_size=30)
plt.errorbar(log10(mhalo_bin),
log10(fj_bin),
yerr=abs(log10(fj_bin) - log10(e_fj_bin)),
c='k',
fmt='o')
if save_plots:
plt.savefig('fj-Mh_all_ref.pdf', bbox_inches='tight')
'''
----------- Kravtsov
'''
fig = plt.figure()
plt.ylabel(r"$\log\rm\,R_e/kpc$", fontsize=16)
plt.xlabel(r"$\log\rm\,r_{\rm vir}/kpc$", fontsize=16)
ax = fig.add_subplot(111)
ax.text(0.1,
0.9,
r"$\rm Sc-Sb$",
fontsize=18,
color='#151AB0',
transform=ax.transAxes)
ax.text(0.1,
0.85,
r"$\rm Sa-S0$",
fontsize=18,
color='#009603',
transform=ax.transAxes)
ax.text(0.1,
0.8,
r"$\rm Es$",
fontsize=18,
color='#BD000D',
transform=ax.transAxes)
# ax.text(0.4, 0.15, r"$\rm Kravtsov Plot$", fontsize=20, transform=ax.transAxes)
# spirals
w = bt < bt_spirals
# plt.plot(log10(r200)[w], log10(Re)[w], 'b.', alpha=0.0075)
x, y, H, lev, _, _, _ = bins_and_hist(r200, Re, w, size_hist, sigs)
# plt.contour(x, y, log10(H).T, levels=lev, colors='#151AB0')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Blues'),
alpha=0.75)
# Sa and lenticulars
w = (bt >= bt_spirals) & (bt < bt_lents)
# plt.plot(log10(r200)[w], log10(Re)[w], 'b.', alpha=0.0075)
x, y, H, lev, _, _, _ = bins_and_hist(r200, Re, w, size_hist, sigs)
# plt.contour(x, y, log10(H).T, levels=lev, colors='#AB9700')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Greens'),
alpha=0.75)
# ellipticals
w = bt > bt_lents
# plt.plot(log10(r200)[w], log10(Re)[w], 'r.', alpha=0.0075)
x, y, H, lev, _, _, _ = bins_and_hist(r200, Re, w, size_hist, sigs)
# plt.contour(x, y, log10(H).T, levels=lev, colors='#BD000D')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Reds'),
alpha=0.75)
plt.plot(log10(linspace(110, 800)),
log10(0.015 * linspace(110, 800)),
'k-',
lw=2)
plt.plot(log10(linspace(110, 800)),
log10(0.015 * linspace(110, 800)) + 0.5,
'k--',
lw=2)
plt.plot(log10(linspace(110, 800)),
log10(0.015 * linspace(110, 800)) - 0.5,
'k--',
lw=2)
plt.xlim([log10(110.), log10(800.)])
# ----- Median relation
x, y, H, lev, r200_bin, Rd_bin, e_Rd_bin = bins_and_hist(r200,
Re,
bt > 0,
size_hist,
sigs,
bin_size=30)
plt.errorbar(log10(r200_bin),
log10(Rd_bin),
yerr=abs(log10(Rd_bin) - log10(e_Rd_bin)),
c='k',
fmt='o')
if save_plots:
plt.savefig('Re-r200_all_ref.pdf', bbox_inches='tight')
'''
----------- Mo, Mao & White Rd-r200
'''
fig = plt.figure()
plt.ylabel(r"$\log\rm\,R_d/kpc$", fontsize=16)
plt.xlabel(r"$\log\rm\,r_{\rm vir}/kpc$", fontsize=16)
ax = fig.add_subplot(111)
ax.text(0.1,
0.9,
r"$\rm Sc-Sb$",
fontsize=18,
color='#151AB0',
transform=ax.transAxes)
ax.text(0.1,
0.85,
r"$\rm Sa-S0$",
fontsize=18,
color='#009603',
transform=ax.transAxes)
# ax.text(0.4, 0.15, r"$\rm Mo, Mao & White Plot$", fontsize=20, transform=ax.transAxes)
# spirals
w = bt < bt_spirals
# plt.plot(log10(r200[w]), log10(Rd[w]), 'b.', alpha=0.01)
x, y, H, lev, r200_bin, Rd_bin, e_Rd_bin = bins_and_hist(
r200, Rd, w, size_hist, sigs)
# plt.errorbar(log10(r200_bin), log10(Rd_bin), yerr=abs(log10(Rd_bin)-log10(e_Rd_bin)), c='b', fmt='o')
# plt.contour(x, y, log10(H).T, levels=lev, colors='#151AB0')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Blues'),
alpha=0.75)
# Sa and lenticulars
w = (bt >= bt_spirals) & (bt < bt_lents)
# plt.plot(log10(r200[w]), log10(Rd[w]), 'y.', alpha=0.01)
x, y, H, lev, r200_bin, Rd_bin, e_Rd_bin = bins_and_hist(
r200, Rd, w, size_hist, sigs)
# plt.errorbar(log10(r200_bin), log10(Rd_bin), yerr=abs(log10(Rd_bin)-log10(e_Rd_bin)), c='g', fmt='o')
# plt.contour(x, y, log10(H).T, levels=lev, colors='#AB9700')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Greens'),
alpha=0.75)
plt.plot(log10(linspace(110, 800)),
log10(0.0112 * linspace(110, 800)),
'k-',
lw=2)
plt.xlim([log10(110.), log10(800.)])
x, y, H, lev, r200_bin, Rd_bin, e_Rd_bin = bins_and_hist(r200,
Rd,
bt < bt_lents,
size_hist,
sigs,
bin_size=30)
plt.errorbar(log10(r200_bin),
log10(Rd_bin),
yerr=abs(log10(Rd_bin) - log10(e_Rd_bin)),
c='k',
fmt='o')
if save_plots:
plt.savefig('Rd-r200_ScS0_ref.pdf', bbox_inches='tight')
'''
----------- sTFR
'''
fig = plt.figure()
plt.ylabel(r"$\log\rm\,M_\ast/M_\odot$", fontsize=16)
plt.xlabel(r"$\log\rm\,V_{max}/km\,s^{-1}$", fontsize=16)
plt.ylim(8, 11.5)
ax = fig.add_subplot(111)
ax.text(0.1,
0.9,
r"$\rm Sc-Sb$",
fontsize=18,
color='#151AB0',
transform=ax.transAxes)
# spirals
w = bt < bt_spirals
# plt.plot(log10(vc[w]), log10(mstar[w]), 'b.', alpha=0.0025)
x, y, H, lev, vc_bin, mstar_bin, e_mstar_bin = bins_and_hist(
vc, mstar, w, size_hist, sigs)
# plt.errorbar(log10(vc_bin), log10(mstar_bin), yerr=abs(log10(mstar_bin)-log10(e_mstar_bin)), c='b', fmt='o')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Blues'))
plt.plot(linspace(1.9, 2.4),
log10(Mstar_TF(linspace(1.9, 2.4))),
'k-',
lw=3)
plt.plot(linspace(1.9, 2.4),
log10(Mstar_TF(linspace(1.9, 2.4))) + 0.15,
'k--',
lw=3)
plt.plot(linspace(1.9, 2.4),
log10(Mstar_TF(linspace(1.9, 2.4))) - 0.15,
'k--',
lw=3)
if save_plots:
plt.savefig('sTF_Sc_ref.pdf', bbox_inches='tight')
'''
----------- Faber-Jackson
'''
fig = plt.figure()
plt.ylabel(r"$\log\rm\,M_\ast/M_\odot$", fontsize=16)
plt.xlabel(r"$\log\rm\,\sigma/km\,s^{-1}$", fontsize=16)
plt.ylim(9, 11.75)
ax = fig.add_subplot(111)
ax.text(0.1,
0.9,
r"$\rm Es$",
fontsize=18,
color='#BD000D',
transform=ax.transAxes)
factor = 1.1 # V_circ(R_50) := factor * sigma(R_50)
# ellipticals
w = bt > bt_lents
# turn vc to sigma for ellipticals
vc[w] /= factor
# Dutton et al. 2010 correction
# (vc[w])[log10(mstar[w]) > 10.5] *= 10.**(0.1-0.3*(log10(mstar[w])[log10(mstar[w]) > 10.5]-10.5))
# (vc[w])[log10(mstar[w]) <= 10.5] *= 10.**0.1
# plt.plot(log10(mstar[w]), log10(vc[w]), 'r.', alpha=0.0025)
x, y, H, lev, vc_bin, mstar_bin, e_mstar_bin = bins_and_hist(
vc, mstar, w, size_hist, sigs)
# plt.errorbar(log10(vc_bin), log10(mstar_bin), yerr=abs(log10(mstar_bin)-log10(e_mstar_bin)), c='r', fmt='o')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Reds'))
plt.plot(linspace(1.8, 2.6),
log10(Mstar_FJ(linspace(1.8, 2.6))),
'k-',
lw=3)
plt.plot(linspace(1.8, 2.6),
log10(Mstar_FJ(linspace(1.8, 2.6))) + 0.1,
'k--',
lw=3)
plt.plot(linspace(1.8, 2.6),
log10(Mstar_FJ(linspace(1.8, 2.6))) - 0.1,
'k--',
lw=3)
if save_plots:
plt.savefig('FJ_Es_ref.pdf', bbox_inches='tight')
'''
----------- FP
'''
fig = plt.figure()
plt.xlabel(r"$\log\rm\,M_\ast/kpc$", fontsize=16)
plt.ylabel(r"$\rm\,10.6+2\log\,\sigma/130\,km\,s^{-1}+\log\,R_e/2\,kpc$",
fontsize=16)
plt.xlim(9, 11.75)
ax = fig.add_subplot(111)
ax.text(0.1,
0.825,
r"$\rm Es$",
fontsize=18,
color='#BD000D',
transform=ax.transAxes)
# etg
w = bt > bt_lents
# fp
fp = 10.6 + 2. * log10(vc[w] / factor / 130.) + log10(Re[w] / 2.)
x, y, H, lev, mstar_bin, fp_bin, e_fp_bin = bins_and_hist(
mstar[w], 10.**fp, mstar[w] > 0, size_hist, sigs)
# plt.errorbar(log10(mstar_bin), fp_bin, yerr=0.5, c='r', fmt='o')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Reds'))
plt.plot(linspace(9, 12), linspace(9, 12), 'k-', lw=3)
plt.plot(linspace(9, 12), linspace(9, 12) + 0.06, 'k--', lw=3)
plt.plot(linspace(9, 12), linspace(9, 12) - 0.06, 'k--', lw=3)
if save_plots:
plt.savefig('FP_Es_ref.pdf', bbox_inches='tight')
'''
----------- Mass - size relation
'''
fig = plt.figure()
plt.xlabel(r"$\log\rm\,M_\ast/kpc$", fontsize=16)
plt.ylabel(r"$\log\rm\,R_e/kpc$", fontsize=16)
plt.xlim(8, 11.75)
ax = fig.add_subplot(111)
ax.text(0.1,
0.9,
r"$\rm Sc-Sb-Sa$",
fontsize=18,
color='#151AB0',
transform=ax.transAxes)
ax.text(0.1,
0.825,
r"$\rm S0-Es$",
fontsize=18,
color='#BD000D',
transform=ax.transAxes)
# spirals
w = bt < bt_ltg
# plt.plot(log10(r200)[w], log10(Re)[w], 'b.', alpha=0.0075)
x, y, H, lev, mstar_bin, Re_bin, e_Re_bin = bins_and_hist(
mstar, Re, w, size_hist, sigs)
# plt.errorbar(log10(mstar_bin), log10(Re_bin), yerr=abs(log10(Re_bin)-log10(e_Re_bin)), c='b', fmt='o')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Blues'),
alpha=0.75)
# ellipticals
w = bt > bt_ltg
# plt.plot(log10(r200)[w], log10(Re)[w], 'r.', alpha=0.0075)
x, y, H, lev, mstar_bin, Re_bin, e_Re_bin = bins_and_hist(
mstar, Re, w, size_hist, sigs)
# plt.errorbar(log10(mstar_bin), log10(Re_bin), yerr=abs(log10(Re_bin)-log10(e_Re_bin)), c='r', fmt='o')
plt.contourf(x,
y,
log10(H).T,
levels=append(lev,
log10(H).max()),
cmap=plt.get_cmap('Reds'),
alpha=0.75)
mass_size_etg = lambda mass: -5.54061 + 0.56 * log10(mass)
mass_size_ltg = lambda mass: -1. + 0.14 * log10(mass) + 0.25 * log10(
1. + mass / 3.98e10)
plt.plot(linspace(9, 11.75), mass_size_etg(logspace(9, 11.75)), 'r-', lw=2)
plt.plot(linspace(9, 11.75),
mass_size_ltg(logspace(9, 11.75)),
'b--',
lw=2)
if save_plots:
plt.savefig('Re-Ms_all_ref.pdf', bbox_inches='tight')
plt.show()
plt.subplot(3, 1, 2)
plt.plot(t, y)
plt.plot(t, y_sol)
plt.xticks(x1, xticks)
plt.yticks(y1, yticks)
plt.ylabel("Y [Km]")
plt.subplot(3, 1, 3)
plt.plot(t, z)
plt.plot(t, z_sol)
plt.xticks(x1, xticks)
plt.yticks(y1, yticks)
plt.ylabel("Z [Km]")
plt.title("Posición en los ejes de coordenadas")
plt.xlabel("Tiempo, t [horas]")
plt.tight_layout()
plt.savefig('grafico_xyz.png')
plt.show()
# Grafico 2
plt.plot(t, lista)
plt.title("Distancia entre posicion real y predicha, δ = 597.9 [km]")
plt.xlabel('Tiempo, t [h]')
plt.ylabel("Deriva [Km]")
plt.xticks(x1, xticks)
plt.savefig('grafico_deriva.png')
plt.show()
import numpy as np
import matplotlib.pylab as plt
#import the data
data = np.transpose(np.loadtxt('data.txt', skiprows=1))
LL = data[0]
energy = data[0] / 8 * .662
counts = data[2]
#----- Plot Lower level vs Counts -----
plt.plot(data[0], counts, 'bo')
plt.xlabel("Lower Level +/- .02")
plt.ylabel("counts +/- 1")
plt.title("CS 137 Radiation Distrobution")
plt.savefig("LL_v_Counts.png")
plt.close()
#----------
#----- plot Energy vs counts -----
plt.plot(energy, counts, 'bo')
plt.xlabel("Energy +/- .003 (MeV)")
plt.ylabel("counts +/- 1")
plt.title("CS 137 Radiation Distrobution")
plt.savefig("Energy_v_Counts.png")
plt.close()
#----------
#computed fit parameters
a1 = 1545
a2 = .658
areas = [17, 18, 19, 37, 20]
# separate plot for each category
for cid, category in enumerate(categories):
print 'Drawing "%s" ...' % category
importance = np.load('%s/%s' % (INDIR, 'FT_feature_importances_ctg%d.npy' % cid))
successful_probes = np.load('%s/%s' % (INDIR, 'FT_successful_probes_ctg%d.npy' % cid))
successful_mnis = np.load('%s/%s' % (INDIR, 'FT_successful_mnis_ctg%d.npy' % cid))
successful_areas = np.load('%s/%s' % (INDIR, 'FT_successful_areas_ctg%d.npy' % cid))
# drop 0,0,0 electrode if it creeps in
drop_idx = np.unique(np.where(successful_mnis == [0, 0, 0])[0])
importance = np.delete(importance, drop_idx, 0)
successful_probes = np.delete(successful_probes, drop_idx, 0)
successful_mnis = np.delete(successful_mnis, drop_idx, 0)
successful_areas = np.delete(successful_areas, drop_idx, 0)
# Mean over each BA
for ba in areas:
if importance[successful_areas == ba, :, :].shape[0] > 0:
fig = plt.figure(figsize=(10, 8), dpi=300);
title = 'Temporal profile of importance for "%s"\nmean over %d probes in BA%d' % (categories[cid], np.sum(successful_areas == ba), ba)
panel_time_profile(np.sum(np.mean(importance[successful_areas == ba, :, :], 0), 0), title, True)
plt.savefig('%s/time_profile_%d_%s_BA%d.png' % (OUTDIR, cid, category, ba), bbox_inches='tight');
plt.clf();
plt.close(fig);
global data
data = load_images('train-images.idx3-ubyte')
def pca(i):
means = mean(data, axis=0)
new_data = data - means
covMat = np.cov(new_data.T)
eigVals, eigVects = np.linalg.eig(covMat)
n_eigValIndice = argsort(-eigVals)
selectedfeature = np.matrix(eigVects.T[n_eigValIndice[:i]])
finalData = new_data * selectedfeature.T
finalData = finalData.real
reconMat = (finalData * selectedfeature) + means
return reconMat, new_data
mse = []
length = 1
for j in range(1, 784, length):
rec, data_aftermean = pca(j)
MSE = mean_squared_error(data_aftermean, np.real(rec))
mse.append(MSE)
plt.plot(mse)
plt.xlabel('d')
plt.ylabel('MSE')
plt.title('MSE against d')
plt.savefig('3c')
plt.show()
ypt + .001,
name,
size=5 + 2 * int(np.round(np.log10(flx))),
color=opts.src_color)
if not opts.nobar: p.colorbar(shrink=.5, format='%.2f')
else: p.subplots_adjust(.05, .05, .95, .95)
def mk_arr(val, dtype=np.double):
if type(val) is np.ndarray: return val.astype(dtype)
return np.array(val, dtype=dtype).flatten()
if opts.outfile != '':
print('Saving to', opts.outfile)
p.savefig(opts.outfile)
else:
# Add right-click functionality for finding locations/strengths in map.
cnt = 1
def click(event):
global cnt
if event.button == 3:
lon, lat = map(event.xdata, event.ydata, inverse=True)
if opts.osys == 'eq': lon = (360 - lon) % 360
lon *= a.img.deg2rad
lat *= a.img.deg2rad
ra, dec = ephem.hours(lon), ephem.degrees(lat)
x, y, z = a.coord.radec2eq((ra, dec))
flx = h[(x, y, z)]
print('#%d (RA,DEC): (%s, %s), Jy: %f' % (cnt, ra, dec, flx))
def plot_gaussian(mu,sigma):
x=[]
y=[]
for i in range(0,mu*3,1):
x.append(i)
y.append(probability_function(i,mu,sigma))
pl.plot(x,y,label='Gaussian'+str(mu))
#Poisson
def poisson(n,mu):
return(math.pow(mu,n)*math.exp(-1*mu)/math.factorial(n))
def plot_poisson(mu):
x=[]
y=[]
for i in range(mu*3):
x.append(i)
y.append(poisson(i,mu))
pl.plot(x,y,label='Poisson'+str(mu))
mu=[1,5,10,20,30]
fig=pl.figure()
pl.xlim(0,60)
for i in mu:
plot_gaussian(i,math.sqrt(i))
plot_poisson(i)
pl.legend()
pl.savefig("Poisson vs Gaussian.pdf")
pl.show()
fig = plt.figure()
ax = Axes3D(fig)
ax.plot_wireframe(grid[0],
grid[1],
mu.reshape(grid[0].shape),
alpha=0.5,
color='g',
label='our estimation')
#ax.plot_wireframe(grid[0], grid[1], reference.reshape(grid[0].shape), alpha=0.5, color='b', label='py reference')
ax.plot_wireframe(grid[0],
grid[1],
original,
alpha=0.5,
color='Orange',
label='real function')
#ax.plot_wireframe(grid[0], grid[1], mu.reshape(grid[0].shape) - reference.reshape(grid[0].shape), alpha=0.5, color='Orange', label='diff mu-reference')
plt.legend()
plt.savefig('fig.png')
# plt.clf()
#plt.imshow((original.flatten()-mu).reshape(24,24), cmap='hot', interpolation='nearest')
#plt.colorbar()
#plt.show()
print("np.linalg.norm(reference-mu) = %lf" % np.linalg.norm(mu - reference))
print(
"np.linalg.norm(original-mu)=%lf, np.linalg.norm(original-reference)=%lf" %
(np.linalg.norm(original.flatten() - mu),
np.linalg.norm(original.flatten() - reference)))
year_path = constants.TASK_1_PATH + str(year) + '/'
create_clean_folders([year_path])
graph, starting_node, colors, labels = graph_to_save_year[year]
pos = nx.spring_layout(graph, k=0.9, iterations=100) # positions for all nodes)
graph: nx.Graph
print(starting_node)
ec = nx.draw_networkx_edges(graph.to_undirected(), pos, alpha=0.2)
nc = nx.draw_networkx_nodes(graph, pos, nodelist=graph.nodes, node_color=colors,
with_labels=True, node_size=100, cmap=cmap, vmin=vmin, vmax=vmax)
lc = nx.draw_networkx_labels(graph, pos, labels, font_size=5)
cb = plt.colorbar(nc)
cb.set_label('Spreading of influence iteration (-1 if not influenced)')
plt.axis('off')
plt.savefig(year_path + str(starting_node), dpi=500)
plt.close()
influenced_path = year_path + 'spreading of influence/'
create_clean_folders([influenced_path])
for el in top_results_year:
topic = el[0]
score = el[1]
topic_path = influenced_path + str(score) + '_' + topic + '/'
create_clean_folders([topic_path])
infl_nodes = influenced_nodes[year][str(year) + '_' + topic]
f = open(topic_path + 'influenced_nodes.txt', "a")
f.write(str(infl_nodes))
f.close()
'''########## SAVE TOPIC MERGES ##########'''
for year in merged_topics_year.keys():
def run_main():
# 1. 准备数据
# 指定股票分析开始日期
start_date = datetime.datetime(2007, 1, 1)
# 指定股票分析截止日期
end_date = datetime.datetime(2017, 3, 1)
# 股票代码
stock_code = '600519.SS' # 沪市贵州茅台
stock_df = pandas_datareader.data.DataReader(stock_code, 'yahoo',
start_date, end_date)
# 预览数据
print(stock_df.head())
# 2. 可视化数据
plt.plot(stock_df['Close'])
plt.title('股票每日收盘价')
plt.show()
# 按周重采样
stock_s = stock_df['Close'].resample('W-MON').mean()
stock_train = stock_s['2014':'2016']
plt.plot(stock_train)
plt.title('股票周收盘价均值')
plt.show()
# 分析 ACF
acf = plot_acf(stock_train, lags=20)
plt.title("股票指数的 ACF")
acf.show()
# 分析 PACF
pacf = plot_pacf(stock_train, lags=20)
plt.title("股票指数的 PACF")
pacf.show()
# 3. 处理数据，平稳化数据
# 这里只是简单第做了一节差分，还有其他平稳化时间序列的方法
# 可以查询资料后改进这里的平稳化效果
stock_diff = stock_train.diff()
diff = stock_diff.dropna()
print(diff.head())
print(diff.dtypes)
plt.figure()
plt.plot(diff)
plt.title('一阶差分')
plt.show()
acf_diff = plot_acf(diff, lags=20)
plt.title("一阶差分的 ACF")
acf_diff.show()
pacf_diff = plot_pacf(diff, lags=20)
plt.title("一阶差分的 PACF")
pacf_diff.show()
# 4. 根据ACF和PACF定阶并建立模型
model = ARIMA(stock_train, order=(1, 1, 1), freq='W-MON')
# 拟合模型
arima_result = model.fit()
print(arima_result.summary())
# 5. 预测
pred_vals = arima_result.predict('20170102',
'20170301',
dynamic=True,
typ='levels')
print(pred_vals)
# 6. 可视化预测结果
stock_forcast = pd.concat([stock_s, pred_vals],
axis=1,
keys=['original', 'predicted'])
plt.figure()
plt.plot(stock_forcast)
plt.title('真实值vs预测值')
plt.savefig('./stock_pred.png', format='png')
plt.show()
reflectance4 = band4.ReadAsArray(0, 0, cols, rows)
reflectance5 = band5.ReadAsArray(0, 0, cols, rows)
reflectance6 = band6.ReadAsArray(0, 0, cols, rows)
reflectance7 = band7.ReadAsArray(0, 0, cols, rows)
reflectance1 = np.array(reflectance1)
reflectance2 = np.array(reflectance2)
reflectance3 = np.array(reflectance3)
reflectance4 = np.array(reflectance4)
reflectance5 = np.array(reflectance5)
reflectance6 = np.array(reflectance6)
reflectance7 = np.array(reflectance7)
plt.imshow(reflectance1, origin='lower left')
plt.colorbar()
plt.savefig('D:\\REFLECTANCE1.jpg') #save the figure
plt.show()
plt.clf()
#read angle data
fn_angle = 'H:/2014MOD09GA006/angle_fin/A2014001_angle_Grid_2D.tif'
ds_angle = gdal.Open(fn_angle, GA_ReadOnly)
#angle1=solar zenith angle, angle2=view zenith angle, angle3=relative azimuth angle
band8 = ds_angle.GetRasterBand(1)
band9 = ds_angle.GetRasterBand(2)
band10 = ds_angle.GetRasterBand(3)
angle1 = band8.ReadAsArray(0, 0, cols, rows)
angle2 = band9.ReadAsArray(0, 0, cols, rows)
angle3 = band10.ReadAsArray(0, 0, cols, rows)
angle1 = np.array(angle1)
def plot_maps(self, df, file_name):
cmap = plt.cm.coolwarm
if self.scenario == 1:
fig, axes = plt.subplots(nrows=2, ncols=1)
# plotting class labels
class_numbers = np.array(df['Class Number'])
width = int(np.sqrt(len(class_numbers)))
class_numbers = np.concatenate(
(class_numbers,
75 * np.ones(width - len(class_numbers) % width))).reshape(
(-1, width))
label_dict = dict([(label, i)
for i, label in enumerate(self.labels)])
label_dict['empty'] = len(label_dict)
rcParams['axes.prop_cycle'] = cycler(
color=cmap(np.linspace(0, 1, len(label_dict))))
axes[0].imshow(class_numbers, cmap=cmap)
# axes[0].legend(handles=patches, loc=2, bbox_to_anchor=(1.01, 1))
axes[0].tick_params(axis='x',
which='both',
bottom=False,
top=False,
labelbottom=False)
axes[0].tick_params(axis='y',
which='both',
left=False,
right=False,
labelleft=False)
# plotting tags
tags = df['Tag']
tags_enum = []
tags_dict = dict([(tag, i)
for i, tag in enumerate(np.unique(self.tags))])
tags_dict['empty'] = len(tags_dict)
for tag in tags:
tags_enum.append(tags_dict[tag])
tags_enum = np.array(tags_enum)
tags_enum = np.concatenate(
(tags_enum, (len(tags_dict) - 1) *
np.ones(width - len(tags_enum) % width))).reshape((-1, width))
rcParams['axes.prop_cycle'] = cycler(
color=cmap(np.linspace(0, 1, len(tags_dict))))
axes[1].imshow(tags_enum, cmap=cmap)
# axes[1].legend(handles=patches, loc=2, bbox_to_anchor=(1.01, 1))
axes[1].tick_params(axis='x',
which='both',
bottom=False,
top=False,
labelbottom=False)
axes[1].tick_params(axis='y',
which='both',
left=False,
right=False,
labelleft=False)
else:
fig, axes = plt.subplots(1, 2, figsize=(6, 12))
class_numbers = np.array(df['Class Number'])
label_dict = dict([(label, i)
for i, label in enumerate(self.labels)])
label_dict['empty'] = len(label_dict)
width = int(np.sqrt(len(class_numbers)))
class_numbers = np.concatenate(
(class_numbers, (len(label_dict) - 1) *
np.ones(width - len(class_numbers) % width))).reshape(
(-1, width))
rcParams['axes.prop_cycle'] = cycler(
color=cmap(np.linspace(0, 1, len(label_dict))))
axes[0].imshow(class_numbers, cmap=cmap)
cmaplist = [cmap(int(i * 3.1)) for i in range(len(label_dict))]
cmaplist[len(label_dict) - 1] = [1.0, 1.0, 1.0, 1.0]
cmap = mpl.colors.LinearSegmentedColormap.from_list(
'Custom cmap', cmaplist, len(label_dict))
axes[0].imshow(class_numbers, cmap=cmap)
patches = [
mpatches.Patch(color=cmap(v), label=k.upper())
for k, v in label_dict.items() if v in class_numbers
]
axes[1].legend(handles=patches, ncol=len(patches) // 20 + 1)
plt.tick_params(axis='x',
which='both',
bottom=False,
top=False,
labelbottom=False)
plt.tick_params(axis='y',
which='both',
left=False,
right=False,
labelleft=False)
plt.savefig(str(file_name))
plt.cla()
return
test_loss, = ax1.plot(test_log['#Iters'], test_log['TestLoss'], linewidth=2, color='green')
ax1.set_ylim(ymin=0, ymax=1)
ax1.set_xlabel('Iterations', fontsize=15)
ax1.set_ylabel('Loss', fontsize=15)
ax1.tick_params(labelsize=15)
#Plotting test accuracy
ax2 = ax1.twinx()
test_accuracy, = ax2.plot(test_log['#Iters'], test_log['TestAccuracy'], linewidth=2, color='blue')
ax2.set_ylim(ymin=0, ymax=1)
ax2.set_ylabel('Accuracy', fontsize=15)
ax2.tick_params(labelsize=15)
#Adding legend
plt.legend([train_loss, test_loss, test_accuracy], ['Training Loss', 'Test Loss', 'Test Accuracy'], bbox_to_anchor=(1, 0.8))
plt.title('Training Curve', fontsize=18)
#Saving learning curve
plt.savefig(learning_curve_path)
'''
Deleting training and test logs
'''
command = 'rm ' + train_log_path
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
process.wait()
command = command = 'rm ' + test_log_path
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
process.wait()
def plot_kin_models(galaxy,
vmode,
vel_ha,
R,
Vrot,
Vrad,
Vtan,
VSYS,
MODEL,
ext,
plot=0,
save=1):
mask_MODEL = np.divide(MODEL, MODEL)
fig = plt.figure(figsize=(6, 2))
gs2 = GridSpec(1, 3)
gs2.update(left=0.06,
right=0.62,
top=0.83,
hspace=0.01,
bottom=0.15,
wspace=0.)
ax = plt.subplot(gs2[0, 0])
ax1 = plt.subplot(gs2[0, 1])
ax2 = plt.subplot(gs2[0, 2])
im0 = ax.imshow(vel_ha - VSYS,
cmap=califa,
origin="lower",
vmin=-250,
vmax=250,
aspect="auto",
extent=ext,
interpolation="nearest")
im2 = ax1.imshow(MODEL,
cmap=califa,
origin="lower",
aspect="auto",
vmin=-250,
vmax=250,
extent=ext,
interpolation="nearest")
residual = (vel_ha * mask_MODEL - VSYS) - MODEL
im2 = ax2.imshow(residual,
cmap=califa,
origin="lower",
aspect="auto",
vmin=-50,
vmax=50,
extent=ext,
interpolation="nearest")
AXIS(ax, tickscolor="k")
AXIS(ax1, tickscolor="k", remove_yticks=True)
AXIS(ax2, tickscolor="k", remove_yticks=True)
ax.set_ylabel(r'$\Delta$ Dec (pix)', fontsize=8, labelpad=0)
ax.set_xlabel(r'$\Delta$ RA (pix)', fontsize=8, labelpad=0)
ax1.set_xlabel(r'$\Delta$ RA (pix)', fontsize=8, labelpad=0)
ax2.set_xlabel(r'$\Delta$ RA (pix)', fontsize=8, labelpad=0)
ax.text(0.05, 0.9, "VLOS", fontsize=7, transform=ax.transAxes)
ax1.text(0.05, 0.9, "MODEL", fontsize=7, transform=ax1.transAxes)
ax2.text(0.05, 0.9, "RESIDUAL", fontsize=7, transform=ax2.transAxes)
ax.set_facecolor('#e8ebf2')
ax1.set_facecolor('#e8ebf2')
ax2.set_facecolor('#e8ebf2')
gs2 = GridSpec(1, 1)
gs2.update(left=0.68, right=0.995, top=0.83, bottom=0.15)
ax3 = plt.subplot(gs2[0, 0])
ax3.plot(R,
Vrot,
color="k",
linestyle='-',
alpha=0.6,
label="V$_\mathrm{circ}$")
ax3.scatter(R, Vrot, color="k", s=5, marker="s")
#ax3.errorbar(R,Vrot, yerr=e_vr, fmt='s', color = "k",markersize = 3, label = "V_\mathrm{circ}")
ax3.plot(R,
Vrad,
color="orange",
linestyle='-',
alpha=0.6,
label="V$_\mathrm{rad}$")
ax3.scatter(R, Vrad, color="orange", s=5, marker="s")
#ax3.errorbar(R,Vrad, yerr=e_Vrad, fmt='s', color = "orange",markersize = 3)
ax3.plot(R,
Vtan,
color="skyblue",
linestyle='-',
alpha=0.6,
label="V$_\mathrm{tan}$")
ax3.scatter(R, Vtan, color="skyblue", s=5, marker="s")
#ax3.errorbar(R,Vtan, yerr=e_Vtan, fmt='s', color = "skyblue",markersize = 3)
ax3.legend(loc="center",
fontsize=6.5,
bbox_to_anchor=(0, 1, 1, 0.1),
ncol=3,
frameon=False)
vels = [Vrot, Vrad, Vtan]
max_vel, min_vel = int(np.nanmax(vels)), int(np.nanmin(vels))
ax3.set_ylim(min_vel - 50, max_vel + 50)
ax3.plot([0, np.nanmax(R)], [0, 0], color="k", linestyle='-', alpha=0.6)
ax3.set_xlabel('r (arcsec)', fontsize=8, labelpad=0)
ax3.set_ylabel('V$_\mathrm{ROT}$ (km/s)', fontsize=8, labelpad=0)
ax3.set_facecolor('#e8ebf2')
AXIS(ax3, tickscolor="k")
cb(im0,
ax,
orientation="horizontal",
colormap=califa,
bbox=(0, 1.12, 1, 1),
width="100%",
height="5%",
label_pad=-23,
label="(km/s)",
font_size=7)
cb(im2,
ax2,
orientation="horizontal",
colormap=califa,
bbox=(0, 1.12, 1, 1),
width="100%",
height="5%",
label_pad=-23,
label="(km/s)",
font_size=7)
if save == 1 and plot == 1:
plt.savefig("./plots/kin_%s_model_%s.png" % (vmode, galaxy), dpi=300)
plt.show()
plt.clf()
else:
if plot == 1:
plt.show()
plt.clf()
if save == 1:
plt.savefig("./plots/kin_%s_model_%s.png" % (vmode, galaxy),
dpi=300)
plt.clf()
BT = BT[:,3,3]
gd = BT > 0
fig, ax = plt.subplots(2, 2)
ax[0,0].plot(BT[gd],'.',markersize=0.5, label='BT (from ME)')
ax[0,0].plot(BT_MMD[gd],'.',markersize=0.5, label='BT (from MMD)')
ax[0,0].legend(markerscale=20, scatterpoints=5, fontsize=8)
ax[0,0].set_ylim(200,320)
ax[0,0].set_xlabel('MM')
ax[0,0].set_ylabel('BT')
ax[1,0].plot(BT_MMD[gd], BT_MMD[gd]-BT[gd],'.',markersize=0.5)
ax[1,0].set_xlim(200,320)
ax[1,0].set_ylim(-1,1)
ax[1,0].set_xlabel('BT_MMD')
ax[1,0].set_ylabel('BT(MMD)-BT(ME)')
# ax[0,1].hist((BT[gd]-float(BT[gd].mean())),bins=100, label='d_BT (from ME)')
# ax[0,1].hist((BT_MMD[gd]-float(BT_MMD[gd].mean())),bins=100, label='d_BT (from MMD)')
# ax[0,1].legend(markerscale=20, scatterpoints=5, fontsize=8)
ax[0,1].hist((BT_MMD[gd]-BT[gd]),bins=100)
ax[0,1].set_xlabel('BT(MMD)-BT(ME)')
ax[1,1].set_ylabel('count (nbins=100)')
ax[1,1].plot(BT_MMD[gd], BT_MMD[gd], '.',markersize=0.5)
ax[1,1].set_xlim(200,320)
ax[1,1].set_ylim(200,320)
ax[1,1].set_xlabel('BT_MMD')
ax[1,1].set_ylabel('BT(ME)')
plt.tight_layout()
plt.savefig('BT_v_BT_MMD.png')
print('** END')
def plot_weights(model,
side='decoder',
title='',
xlabel='',
comp=None,
rotation=15,
fig_path=None):
try:
model.n_channels = model.n_datasets
except:
pass
if not hasattr(model, 'ch_name'):
model.ch_name = [f'Ch.{_}' for _ in range(model.n_channels)]
fig, axs = plt.subplots(model.n_channels, 1)
if comp is None:
suptitle = 'Model Weights\n({})'.format(side)
else:
suptitle = 'Model Weights\n({}, comp. {})'.format(side, comp)
plt.suptitle(title + suptitle)
for ch in range(model.n_channels):
ax = axs if model.n_channels == 1 else axs[
ch] # 'AxesSubplot' object does not support indexing
x = np.arange(model.n_feats[ch])
if side == 'encoder':
y = model.vae[ch].W_mu.weight.detach().numpy().T.copy()
else:
y = model.vae[ch].W_out.weight.detach().numpy().copy()
try: # In case of bernoulli features
if model.bern_feats is not None:
bidx = model.bern_feats[ch]
y[bidx, :] = sigmoid(y[bidx, :])
except:
pass
if y.shape[0] > 200:
pass
else:
if comp is not None:
y = y[:, comp]
# axs[ch].plot(y)
if model.lat_dim == 1 or comp is not None:
ax.bar(x, y.reshape(-1), width=0.25)
else:
ax.plot(x, y)
ax.set_ylabel(model.ch_name[ch], rotation=45, fontsize=14)
if comp is None:
ax.legend(['comp. ' + str(c) for c in range(model.lat_dim)])
ax.axhline(y=0, ls="--", c=".3")
try:
tick_marks = np.arange(len(model.varname[ch]))
ax.set_xticks(tick_marks)
ax.set_xticklabels(model.varname[ch],
rotation=rotation,
fontsize=20)
except:
pass
plt.xlabel(xlabel)
if fig_path is not None:
pickle.dump(fig, open(fig_path + '.pkl', 'wb'))
fsch = 4 * model.n_channels
fsfeat = 3 * max(model.n_feats)
plt.rcParams['figure.figsize'] = (fsfeat, fsch)
plt.tight_layout()
plt.savefig(fig_path, bbox_inches='tight')
plt.close()
mpl.rcParams['xtick.major.width'] = 5
mpl.rcParams['xtick.minor.size'] = 10
mpl.rcParams['xtick.minor.width'] = 5
plt.rcParams['xtick.labelsize'] = 20
mpl.rcParams['ytick.major.size'] = 10
mpl.rcParams['ytick.major.width'] = 5
mpl.rcParams['ytick.minor.size'] = 10
mpl.rcParams['ytick.minor.width'] = 5
plt.rcParams['ytick.labelsize'] = 20
fig = plt.figure(figsize=(10, 10))
thefile = "One_Bar_Dynamics_Dynamic_Vibration.h5.feioutput"
finput = h5py.File(thefile)
# Read the time and displacement
times = finput["time"][:]
disp = finput["/Model/Nodes/Generalized_Displacements"][5, :]
# Configure the figure filename, according to the input filename.
outfig = thefile.replace("_", "-")
outfigname = outfig.replace("h5.feioutput", "pdf")
# Plot the figure. Add labels and titles.
plt.plot(times, disp, Linewidth=4)
plt.grid()
plt.xlabel("Time [s] ")
plt.ylabel("Displacement [m] ")
plt.savefig(outfigname, bbox_inches='tight')
plt.show()
]
plt.xlabel('Epochs')
plt.ylabel('CTC Loss')
x_axis = list(range(1, 21))
plt.plot(x_axis, t_loss_1, 'b', label='LSTM-50 training loss')
plt.plot(x_axis, t_loss_2, 'g', label='GRU-50 training loss')
plt.plot(x_axis, v_loss_1, 'b-.', label='LSTM-50 validation loss')
plt.plot(x_axis, v_loss_2, 'g-.', label='GRU-50 validation loss')
plt.legend()
plt.xticks(x_axis)
#plt.show()
plt.savefig('50neurons-loss.png', dpi=600)
#100units
#lstm
t_loss_1 = [
307, 197, 187, 193, 208, 208, 207, 206, 206, 204, 196, 183, 176, 174, 167,
161, 156, 154, 149, 159
]
v_loss_1 = [
303, 289, 249, 278, 278, 278, 276, 277, 279, 276, 259, 287, 245, 236, 225,
230, 232, 212, 214, 230
]
#gru
t_loss_2 = [
def plot_latent_space(model,
data=None,
qzx=None,
classificator=None,
text=None,
uncertainty=True,
comp=None,
fig_path=None):
if data is None:
try:
data = model.data
except:
pass
channels = model.n_channels
if not hasattr(model, 'ch_name'):
model.ch_name = [f'Ch.{_}' for _ in range(channels)]
comps = model.lat_dim
# output = model(data)
# qzx = output['qzx']
if qzx is None:
qzx = model.encode(data)
if classificator is not None:
groups = np.unique(classificator)
if not groups.dtype == np.dtype('O'):
# remove nans if groups are not objects (strings)
groups = groups[~np.isnan(groups)]
# One figure per latent component
# Linear relationships expected between channels
if comp is not None:
itercomps = comp if isinstance(comp, list) else [comp]
else:
itercomps = range(comps)
# One figure per channel
# Uncorrelated relationsips expected between latent components
for comp in itercomps:
fig, axs = plt.subplots(channels, channels)
fig.suptitle(r'$z_{' + str(comp) + '}$', fontsize=30)
for i, j in itertools.product(range(channels), range(channels)):
if i == j:
axs[j, i].text(0.5,
0.5,
f'z|{model.ch_name[i]}',
horizontalalignment='center',
verticalalignment='center',
fontsize=20)
axs[j, i].axis('off')
elif i > j:
xi = qzx[i].loc.detach().numpy()[:, comp]
xj = qzx[j].loc.detach().numpy()[:, comp]
si = np.exp(0.5 * qzx[i].scale.detach().numpy()[:, comp])
sj = np.exp(0.5 * qzx[j].scale.detach().numpy()[:, comp])
ells = [
Ellipse(xy=[xi[p], xj[p]],
width=2 * si[p],
height=2 * sj[p]) for p in range(len(xi))
]
if classificator is not None:
for g in groups:
g_idx = classificator == g
axs[j, i].plot(xi[g_idx],
xj[g_idx],
'.',
alpha=0.5,
markersize=15)
if uncertainty:
color = ax.get_lines()[-1].get_color()
for idx in np.where(g_idx)[0]:
axs[j, i].add_artist(ells[idx])
ells[idx].set_alpha(0.1)
ells[idx].set_facecolor(color)
else:
axs[j, i].plot(xi, xj, '.')
if uncertainty:
for e in ells:
axs[j, i].add_artist(e)
e.set_alpha(0.1)
if text is not None:
[axs[j, i].text(*item) for item in zip(xi, xj, text)]
# Bisettrice
lox, hix = axs[j, i].get_xlim()
loy, hiy = axs[j, i].get_ylim()
lo, hi = np.min([lox, loy]), np.max([hix, hiy])
axs[j, i].plot([lo, hi], [lo, hi], ls="--", c=".3")
else:
axs[j, i].axis('off')
if classificator is not None:
[axs[-1, 0].plot(0, 0) for g in groups]
legend = [
'{} (n={})'.format(g, len(classificator[classificator == g]))
for g in groups
]
axs[-1, 0].legend(legend)
try:
axs[-1, 0].set_title(classificator.name)
except AttributeError:
axs[-1, 0].set_title('Groups')
if fig_path is not None:
pickle.dump(fig, open(fig_path + '.pkl', 'wb'))
fs = 2 * channels + 1
plt.rcParams['figure.figsize'] = (fs, fs)
# plt.tight_layout()
plt.savefig(fig_path, bbox_inches='tight')
plt.close()
return fig, axs
# Output information
print 'TTV amplitude =', numpy.amax(ttv_array), \
'[min] = ', numpy.amax(ttv_array) * 60, '[sec]'
print 'TDV amplitude =', numpy.amax(tdv_array), \
'[min] = ', numpy.amax(tdv_array) * 60, '[sec]'
ax = plt.axes()
plt.plot(ttv_array, tdv_array, color='k')
plt.rc('font', **{'family': 'serif', 'serif': ['Computer Modern']})
plt.rc('text', usetex=True)
plt.tick_params(axis='both', which='major', labelsize=16)
plt.xlabel('transit timing variation [minutes]', fontsize=16)
plt.ylabel('transit duration variation [minutes]', fontsize=16)
ax.tick_params(direction='out')
plt.ylim([numpy.amin(tdv_array) * 1.2, numpy.amax(tdv_array) * 1.2])
plt.xlim([numpy.amin(ttv_array) * 1.2, numpy.amax(ttv_array) * 1.2])
plt.plot((0, 0), (numpy.amax(tdv_array) * 10., numpy.amin(tdv_array) * 10.),
'k',
linewidth=0.5)
plt.plot((numpy.amin(ttv_array) * 10., numpy.amax(ttv_array) * 10.), (0, 0),
'k',
linewidth=0.5)
# Fix axes for comparison with eccentric moon
plt.xlim(-0.15, +0.15)
plt.ylim(-0.65, +0.65)
plt.annotate(r"4:2:1", xy=(-0.145, +0.55), size=16)
plt.savefig("fig_system_8.eps", bbox_inches='tight')
if hzdict[label]==t0:
ax.set_xlim(min(times)-(max(times)-min(times))*0.05,max(times)+(max(times)-min(times))*0.05)
elif hzdict[label]==t1:
ax.set_xlim(dt.datetime.strptime(max_times_str,date_fmt)-dt.timedelta(minutes=hzdict[label])-dt.timedelta(minutes=hzdict[label])*0.05,dt.datetime.strptime(max_times_str,date_fmt)+dt.timedelta(minutes=hzdict[label]*0.05))
else:
ax.set_xlim(dt.datetime.strptime(max_times_str,date_fmt)-dt.timedelta(hours=hzdict[label])-dt.timedelta(hours=hzdict[label])*0.05,dt.datetime.strptime(max_times_str,date_fmt)+dt.timedelta(hours=hzdict[label]*0.05))
plt.draw()
radio.on_clicked(hzfunc)
for k in range(6):
ax.plot(times,pressures[k],label=labels[k+1]+' %.2e mbar'%pressures[k][-1],color=col[k],marker='.',ms=mars,ls=lines)
''' plots vertical lines when label is changed '''
"""for i in range(len(events)):
ax.plot([events[i],events[i]], [1e-12,1e2], 'k', lw = 1)
ax.text(events[i],1e1,'Label changed')"""
ax.set_yscale('log')
ax.set_ylim(1e-12,1e2)
ax.grid(True,which='both',ls='-',color='0.45')
fig.autofmt_xdate()
ax.format_xdata = mdate.DateFormatter('%d')
ax.xaxis.set_major_formatter(myFMT)
ax.set_ylabel('Pressure [mbar]')
lgnd=ax.legend(loc=3)
for i in range(6):
lgnd.legendHandles[i]._legmarker.set_markersize(5)
datenow = str(dt.datetime.now().strftime(date_fmt))
plt.savefig('pressure - %s.png'%datenow.replace(':','-'))
plt.show()