def avg_region(self,
la_lim,
lo_lim,
nla=100,
nlo=100,
stellar_grid=False,
reflection=False,
temp_map=True):
las = np.linspace(la_lim[0], la_lim[1], nla)
los = np.linspace(lo_lim[0], lo_lim[1], nlo)
for i in range(0, len(los)):
if los[i] > np.pi:
los[i] -= 2 * np.pi
if los[i] < -np.pi:
los[i] += 2 * np.pi
tot_flux = 0.0
tot_weight = 0.0
for la in las:
weight = np.cos(la)
for lo in los:
flux = sp.call_map_model(self, la, lo)
if temp_map == False:
tot_flux += weight * flux[0]
else:
tot_flux += weight * flux[1]
tot_weight += weight
avg = tot_flux / tot_weight
return avg
def find_temp(self,
p0,
sign,
stellar_grid=False,
reflection=False,
temp_map=True):
out = minimize(self.find_func,
p0,
method='L-BFGS-B',
bounds=((-np.pi / 2, np.pi / 2), (None, None)),
args=(sign, temp_map))
p = out['x']
if p[1] > np.pi:
revs = math.ceil(abs(p[1] / (2 * np.pi)))
p[1] -= revs * 2 * np.pi
if p[1] < -np.pi:
revs = (math.ceil(abs(p[1] / (2 * np.pi)))) - 1
p[1] += revs * 2 * np.pi
flux = sp.call_map_model(self, p[0], p[1])
if temp_map == True:
f = flux[1]
else:
f = flux[0]
return (f, out['x'] * 180 / np.pi)
def avg_region(self,la_lim,lo_lim,nla=100,nlo=100,stellar_grid=False,reflection=False,temp_map=True,pweight=1):
las = np.linspace(la_lim[0],la_lim[1],nla)
los = np.linspace(lo_lim[0],lo_lim[1],nlo)
for i in range(0,len(los)):
if los[i] > np.pi:
los[i] -= 2*np.pi
if los[i] < -np.pi:
los[i] += 2*np.pi
tot_flux = 0.0
tot_weight = 0.0
for la in las:
weight = np.cos(la)
for lo in los:
flux = sp.call_map_model(self,la,lo)
if temp_map == False:
tot_flux += weight*flux[0]
else:
tot_flux += weight*(flux[1]**pweight)
tot_weight += weight
avg = tot_flux/tot_weight
avg = avg**(1.0/pweight)
return avg
def find_func(self, x, sign, temp_map):
if x[1] > np.pi:
revs = math.ceil(abs(x[1] / (2 * np.pi)))
x[1] -= revs * 2 * np.pi
if x[1] < -np.pi:
revs = (math.ceil(abs(x[1] / (2 * np.pi)))) - 1
x[1] += revs * 2 * np.pi
flux = sp.call_map_model(self, x[0], x[1])
if temp_map == True:
return sign * flux[1]
else:
return sign * flux[0]
def find_func(self,x,sign,temp_map):
if x[1] > np.pi:
revs = math.ceil(abs(x[1]/(2*np.pi)))
x[1] -= revs*2*np.pi
if x[1] < -np.pi:
revs = (math.ceil(abs(x[1]/(2*np.pi))))-1
x[1] += revs*2*np.pi
flux = sp.call_map_model(self,x[0],x[1])
if temp_map == True:
return sign*flux[1]
else:
return sign*flux[0]
def find_temp(self,p0,sign,stellar_grid=False,reflection=False,temp_map=True):
out = minimize(self.find_func,p0,method='L-BFGS-B',bounds=((-np.pi/2,np.pi/2),(None,None)),args=(sign,temp_map))
p = out['x']
if p[1] > np.pi:
revs = math.ceil(abs(p[1]/(2*np.pi)))
p[1] -= revs*2*np.pi
if p[1] < -np.pi:
revs = (math.ceil(abs(p[1]/(2*np.pi))))-1
p[1] += revs*2*np.pi
flux = sp.call_map_model(self,p[0],p[1])
if temp_map == True:
f = flux[1]
else:
f = flux[0]
return(f,out['x']*180/np.pi)
def plot_square(spider_params,
ax=False,
min_temp=False,
max_temp=False,
temp_map=False,
min_bright=0.2,
scale_planet=1.0,
planet_cen=[0.0, 0.0],
mycmap=plt.get_cmap('inferno'),
show_cax=True,
theme='white',
show_axes=True,
nla=100,
nlo=100):
if theme == 'black':
bg = 'black'
tc = ("#04d9ff")
else:
bg = 'white'
tc = 'black'
if ax == False:
f, ax = plt.subplots(facecolor=bg)
new_ax = True
else:
new_ax = False
las = np.linspace(-np.pi / 2, np.pi / 2, nla)
los = np.linspace(-np.pi, np.pi, nlo)
plt.ylim(-90, 90)
plt.xlim(-180, 180)
fluxes = []
for la in las:
row = []
for lo in los:
flux = sp.call_map_model(spider_params, la, lo)
if temp_map == False:
row += [flux[0]]
else:
row += [flux[1]]
fluxes += [row]
fluxes = np.array(fluxes)
if temp_map == False:
fluxes = fluxes / np.max(fluxes)
lala, lolo = np.meshgrid(los, las)
plt.plot([0], [0], 'x', color=('#0cff0c'), ms=10, mew=2)
ax.set_xlabel('longitude', color=tc)
ax.set_ylabel('latitude', color=tc)
ax.set_axis_bgcolor(bg)
if show_axes == False:
ax.spines['bottom'].set_color(bg)
ax.spines['left'].set_color(bg)
ax.spines['top'].set_color(bg)
ax.spines['right'].set_color(bg)
else:
ax.spines['bottom'].set_color(tc)
ax.spines['left'].set_color(tc)
ax.spines['top'].set_color(tc)
ax.spines['right'].set_color(tc)
if show_axes == False:
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
else:
ax.get_xaxis().set_visible(True)
ax.get_yaxis().set_visible(True)
ax.tick_params(colors=tc)
if show_cax == True:
cax = plt.pcolor(lala * 180 / np.pi,
lolo * 180 / np.pi,
fluxes,
cmap=mycmap)
# cbar = plt.colorbar(mycax, cax=cax,ticks=[1100,1300,1500,1700,1900])
cbar = plt.colorbar()
cbar.ax.tick_params(colors=tc)
if temp_map == True:
cbar.set_label('T (K)', color=tc) # horizontal colorbar
else:
cbar.set_label('Relative brightness',
color=tc) # horizontal colorbar
return ax
if temp_map == True:
b_i = 17
else:
b_i = 16
if min_temp == False:
temps = planet[:, b_i]
min_temp = np.min(temps)
max_temp = np.max(temps)
dp = ((max_temp - min_temp) * min_bright)
for j in range(0, len(planet)):
val = (dp + planet[j][b_i] - min_temp) / (dp + max_temp - min_temp)
c = mycmap(val)
n = planet[j]
r1 = n[13] * scale_planet
r2 = n[14] * scale_planet
radii = [r1, r2]
thetas = np.linspace(n[10], n[11], 100)
xs = np.outer(radii, np.cos(thetas)) + planet_cen[0]
ys = np.outer(radii, np.sin(thetas)) + planet_cen[1]
xs[1, :] = xs[1, ::-1]
ys[1, :] = ys[1, ::-1]
ax.fill(np.ravel(xs), np.ravel(ys), edgecolor=c, color=c, zorder=2)
divider = make_axes_locatable(ax)
# Append axes to the right of ax, with 20% width of ax
# zero_temp = min_temp - dp
zero_temp = min_temp
data = [np.linspace(zero_temp, max_temp, 1000)] * 2
fake, fake_ax = plt.subplots()
mycax = fake_ax.imshow(data, interpolation='none', cmap=mycmap)
plt.close(fake)
return ax
def retrieve_map_full_samples(degree=3,dataDir="data/sph_harmonic_coefficients_full_samples/hotspot/",isspider=True):
tmp = np.load("{}spherearray_deg_{}.npz".format(dataDir,degree))
outDictionary = tmp['arr_0'].tolist()
londim = 100
latdim = 100
samples = outDictionary['spherical coefficients'] # output from eigencurves
waves = outDictionary['wavelength (um)']
bestsamples=outDictionary['best fit coefficients'] # best fit sample from eigencurves
randomIndices = np.random.randint(0,len(samples),39)
nRandom = len(randomIndices)
fullMapArray = np.zeros([nRandom,len(waves),londim,latdim])
bestMapArray = np.zeros([len(waves),londim,latdim])
#SPIDERMAN stuff added by Megan
if isspider:
params0=sp.ModelParams(brightness_model='spherical')
params0.nlayers=20
params0.t0=-2.21857/2.
params0.per=2.21857567
params0.a_abs=0.0313
params0.inc=85.71
params0.ecc=0.0
params0.w=90.
params0.rp=0.155313
params0.a=8.863
params0.p_u1=0.
params0.p_u2=0.
params0.degree=degree
params0.la0=0.
params0.lo0=0.
if not isspider:
inputArr=np.zeros([len(waves),bestsamples.shape[0]+1])
inputArr[:,0] = waves
inputArr[:,1:] = bestsamples.transpose()
wavelengths, lats, lons, maps = eigenmaps.generate_maps(inputArr,N_lon=londim, N_lat=latdim)
bestMapArray=maps
else:
for i in np.arange(np.shape(waves)[0]):
params0.sph=list(bestsamples[:,i])
nla=latdim
nlo=londim
las = np.linspace(-np.pi/2,np.pi/2,nla)
los = np.linspace(-np.pi,np.pi,nlo)
fluxes = []
for la in las:
row = []
for lo in los:
flux = sp.call_map_model(params0,la,lo)
row += [flux[0]]
fluxes += [row]
fluxes = np.array(fluxes)
lons, lats = np.meshgrid(los,las)
bestMapArray[i,:,:] = fluxes
for drawInd, draw in enumerate(samples[randomIndices]):
if not isspider:
inputArr = np.zeros([len(waves),samples.shape[1]+1])
inputArr[:,0] = waves
inputArr[:,1:] = draw.transpose()
wavelengths, lats, lons, maps = eigenmaps.generate_maps(inputArr,
N_lon=londim, N_lat=latdim)
fullMapArray[drawInd,:,:,:] = maps
#MEGAN ADDED STUFF
else:
for i in np.arange(np.shape(waves)[0]):
params0.sph=list(samples[drawInd,:,i])
nla=latdim
nlo=londim
las = np.linspace(-np.pi/2,np.pi/2,nla)
los = np.linspace(-np.pi,np.pi,nlo)
fluxes = []
for la in las:
row = []
for lo in los:
flux = sp.call_map_model(params0,la,lo)
row += [flux[0]]
fluxes += [row]
fluxes = np.array(fluxes)
lons, lats = np.meshgrid(los,las)
#print(np.min(lats),np.min(lons),np.min(las),np.min(los))
#lats, lons, maps = testgenmaps.spmap(inputArr,londim, latdim)
fullMapArray[drawInd,i,:,:] = fluxes
## note that the maps have the origin at the top
## so we have to flip the latitude array
lats = np.flip(lats,axis=0)
return fullMapArray, bestMapArray, lats, lons, waves
def find_groups(dataDir,ngroups=4,degree=2,
londim=100, latdim=100,
trySamples=45,extent=0.5,sortMethod='avg',isspider=True):
"""
Find the eigenspectra using k means clustering
Parameters
----------
ngroups: int
Number of eigenspectra to group results into
degree: int
Spherical harmonic degree to draw samples from
testNum: int
Test number (ie. lightcurve number 1,2, etc.)
trySamples: int
Number of samples to find groups with
All samples take a long time so this takes a random
subset of samples from which to draw posteriors
sortMethod: str
Method to sort the groups returned by K means clustering
None, will not sort the output
'avg' will sort be the average of the spectrum
'middle' will sort by the flux in the middle of the spectrum
extent: time covered by the eclipse/phase curve.
Sets what portion of the map is used for clustering (e.g. full planet or dayside only)
"""
#samplesDir = "data/sph_harmonic_coefficients_full_samples"
#dataDir = "{}/eclipse_lightcurve_test{}/".format(samplesDir,testNum)
tmp = np.load("{}spherearray_deg_{}.npz".format(dataDir,degree))
outDictionary = tmp['arr_0'].tolist()
samples = outDictionary['spherical coefficients'] # output from eigencurves
if trySamples>len(samples):
assert(trySamples<=len(samples)),("trySamples must be less than the total number of MCMC samples, "+str(len(samples)))
eigenspectra_draws = []
kgroup_draws = []
uber_eigenlist=[[[[] for i in range(10)] for i in range(ngroups)] for i in range(trySamples)]
if isspider:
params0=sp.ModelParams(brightness_model='spherical') #megan added stuff
params0.nlayers=20
params0.t0=-2.21857/2.
params0.per=2.21857567
params0.a_abs=0.0313
params0.inc=85.71
params0.ecc=0.0
params0.w=90.
params0.rp=0.155313
params0.a=8.863
params0.p_u1=0.
params0.p_u2=0.
params0.degree=degree
params0.la0=0.
params0.lo0=0.
waves=np.array([2.41,2.59,2.77,2.95,3.13,3.31,3.49,3.67,3.85,4.03])
minlon=np.around(extent/2.*londim)
#print(minlon)
randomIndices = np.random.randint(0,len(samples),trySamples)
for drawInd,draw in enumerate(samples[randomIndices]):
## Re-formatting here into a legacy system
## 1st dimension is wavelength
## 2nd dimensions is data (0th element = wavelength)
## (1: elements are spherical harmonic coefficients)
if not isspider:
inputArr = np.zeros([10,samples.shape[1]+1])
inputArr[:,0] = np.array([2.41,2.59,2.77,2.95,3.13,3.31,3.49,3.67,3.85,4.03])
inputArr[:,1:] = draw.transpose()
waves, lats, lons, maps = eigenmaps.generate_maps(inputArr, N_lon=londim, N_lat=latdim)
maps=maps[:,:,int(londim/2.-minlon):int(londim/2.+minlon)]
#maps=np.zeros((np.shape(waves)[0],londim,latdim)) #full map
else:
maps=np.zeros((np.shape(waves)[0],latdim,int(minlon*2))) #only dayside
#print(np.shape(maps))
for i in np.arange(np.shape(waves)[0]):
params0.sph=list(samples[drawInd,:,i])
nla=latdim
nlo=londim
las = np.linspace(-np.pi/2,np.pi/2,nla)
los = np.linspace(-np.pi,np.pi,nlo)
fluxes = []
for la in las:
row = []
for lo in los:
flux = sp.call_map_model(params0,la,lo)
row += [flux[0]]
fluxes += [row]
fluxes = np.array(fluxes)
lons, lats = np.meshgrid(los,las)
#print(np.min(lats),np.min(lons),np.min(las),np.min(los))
#lats, lons, maps = testgenmaps.spmap(inputArr,londim, latdim)
#pdb.set_trace()
maps[i,:,:] = fluxes[:,int(londim/2.-minlon):int(londim/2.+minlon)]
kgroups = kmeans.kmeans(maps, ngroups)
eigenspectra,eigenlist = bin_eigenspectra.bin_eigenspectra(maps, kgroups)
eigenspectra_draws.append(eigenspectra)
kgroup_draws.append(kgroups)
for groupind in range(ngroups):
for waveind in range(10):
uber_eigenlist[drawInd][groupind][waveind]=eigenlist[groupind][waveind,:]
if sortMethod is not None:
eigenspectra_draws_final, kgroup_draws_final,uber_eigenlist_final = kmeans.sort_draws(eigenspectra_draws,
kgroup_draws,uber_eigenlist,
method=sortMethod)
else:
eigenspectra_draws_final, kgroup_draws_final,uber_eigenlist_final = eigenspectra_draws, kgroup_draws,uber_eigenlist
return eigenspectra_draws_final, kgroup_draws_final,uber_eigenlist_final, maps
def plot_square(spider_params,ax=False,min_temp=False,max_temp=False,temp_map=False,min_bright=0.2,scale_planet=1.0,planet_cen=[0.0,0.0],mycmap=plt.get_cmap('inferno'),show_cax=True,theme='white',show_axes=True,nla=100,nlo=100):
if theme == 'black':
bg = 'black'
tc = ("#04d9ff")
else:
bg = 'white'
tc = 'black'
if ax == False:
f, ax = plt.subplots(facecolor=bg)
new_ax = True
else:
new_ax = False
las = np.linspace(-np.pi/2,np.pi/2,nla)
los = np.linspace(-np.pi,np.pi,nlo)
plt.ylim(-90,90)
plt.xlim(-180,180)
fluxes = []
for la in las:
row = []
for lo in los:
flux = sp.call_map_model(spider_params,la,lo)
if temp_map == False:
row += [flux[0]]
else:
row += [flux[1]]
fluxes += [row]
fluxes = np.array(fluxes)
if temp_map == False:
fluxes = fluxes/np.max(fluxes)
lala, lolo = np.meshgrid(los,las)
plt.plot([0],[0],'x',color=('#0cff0c'),ms=10,mew=2)
ax.set_xlabel('longitude',color=tc)
ax.set_ylabel('latitude',color=tc)
ax.set_axis_bgcolor(bg)
if show_axes == False:
ax.spines['bottom'].set_color(bg)
ax.spines['left'].set_color(bg)
ax.spines['top'].set_color(bg)
ax.spines['right'].set_color(bg)
else:
ax.spines['bottom'].set_color(tc)
ax.spines['left'].set_color(tc)
ax.spines['top'].set_color(tc)
ax.spines['right'].set_color(tc)
if show_axes == False:
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
else:
ax.get_xaxis().set_visible(True)
ax.get_yaxis().set_visible(True)
ax.tick_params(colors=tc)
if show_cax == True:
cax = plt.pcolor(lala*180/np.pi,lolo*180/np.pi,fluxes,cmap=mycmap)
# cbar = plt.colorbar(mycax, cax=cax,ticks=[1100,1300,1500,1700,1900])
cbar = plt.colorbar()
cbar.ax.tick_params(colors=tc)
if temp_map == True:
cbar.set_label('T (K)',color=tc) # horizontal colorbar
else:
cbar.set_label('Relative brightness',color=tc) # horizontal colorbar
return ax
if temp_map == True:
b_i = 17
else:
b_i = 16
if min_temp == False:
temps = planet[:,b_i]
min_temp = np.min(temps)
max_temp = np.max(temps)
dp = ((max_temp-min_temp)*min_bright)
for j in range (0,len(planet)):
val = (dp + planet[j][b_i]-min_temp)/(dp + max_temp-min_temp)
c = mycmap(val)
n = planet[j]
r1 = n[13]*scale_planet
r2 = n[14]*scale_planet
radii = [r1,r2]
thetas = np.linspace(n[10],n[11],100)
xs = np.outer(radii, np.cos(thetas)) + planet_cen[0]
ys = np.outer(radii, np.sin(thetas)) + planet_cen[1]
xs[1,:] = xs[1,::-1]
ys[1,:] = ys[1,::-1]
ax.fill(np.ravel(xs), np.ravel(ys), edgecolor=c,color=c,zorder=2)
divider = make_axes_locatable(ax)
# Append axes to the right of ax, with 20% width of ax
# zero_temp = min_temp - dp
zero_temp = min_temp
data = [np.linspace(zero_temp,max_temp,1000)]*2
fake, fake_ax = plt.subplots()
mycax = fake_ax.imshow(data, interpolation='none', cmap=mycmap)
plt.close(fake)
return ax