def romanzuniga07(wavelength, AKs, makePlot=False):
filters = ['J', 'H', 'Ks', '[3.6]', '[4.5]', '[5.8]', '[8.0]']
wave = np.array([1.240, 1.664, 2.164, 3.545, 4.442, 5.675, 7.760])
A_AKs = np.array([2.299, 1.550, 1.000, 0.618, 0.525, 0.462, 0.455])
A_AKs_err = np.array([0.530, 0.080, 0.000, 0.077, 0.063, 0.055, 0.059])
# Interpolate over the curve
spline_interp = interpolate.splrep(wave, A_AKs, k=3, s=0)
A_AKs_at_wave = interpolate.splev(wavelength, spline_interp)
A_at_wave = AKs * A_AKs_at_wave
if makePlot:
py.clf()
py.errorbar(wave, A_AKs, yerr=A_AKs_err, fmt='bo',
markerfacecolor='none', markeredgecolor='blue',
markeredgewidth=2)
# Make an interpolated curve.
wavePlot = np.arange(wave.min(), wave.max(), 0.1)
extPlot = interpolate.splev(wavePlot, spline_interp)
py.loglog(wavePlot, extPlot, 'k-')
# Plot a marker for the computed value.
py.plot(wavelength, A_AKs_at_wave, 'rs',
markerfacecolor='none', markeredgecolor='red',
markeredgewidth=2)
py.xlabel('Wavelength (microns)')
py.ylabel('Extinction (magnitudes)')
py.title('Roman Zuniga et al. 2007')
return A_at_wave
def test1():
import numpy as np
import pylab
from scipy import sparse
from regreg.algorithms import FISTA
from regreg.atoms import l1norm
from regreg.container import container
from regreg.smooth import quadratic
Y = np.random.standard_normal(500); Y[100:150] += 7; Y[250:300] += 14
sparsity = l1norm(500, lagrange=1.0)
#Create D
D = (np.identity(500) + np.diag([-1]*499,k=1))[:-1]
D = sparse.csr_matrix(D)
fused = l1norm.linear(D, lagrange=19.5)
loss = quadratic.shift(-Y, lagrange=0.5)
p = container(loss, sparsity, fused)
soln1 = blockwise([sparsity, fused], Y)
solver = FISTA(p)
solver.fit(max_its=800,tol=1e-10)
soln2 = solver.composite.coefs
#plot solution
pylab.figure(num=1)
pylab.clf()
pylab.scatter(np.arange(Y.shape[0]), Y, c='r')
pylab.plot(soln1, c='y', linewidth=6)
pylab.plot(soln2, c='b', linewidth=2)
def plot_stress(self, block_ids=None, fignum=0):
block_ids = self.check_block_ids_list(block_ids)
#
plt.figure(fignum)
ax1=plt.gca()
plt.clf()
plt.figure(fignum)
plt.clf()
ax0=plt.gca()
#
for block_id in block_ids:
rws = numpy.core.records.fromarrays(zip(*filter(lambda x: x['block_id']==block_id, self.shear_stress_sequences)), dtype=self.shear_stress_sequences.dtype)
stress_seq = []
for rw in rws:
stress_seq += [[rw['sweep_number'], rw['shear_init']]]
stress_seq += [[rw['sweep_number'], rw['shear_final']]]
X,Y = zip(*stress_seq)
#
ax0.plot(X,Y, '.-', label='block_id: %d' % block_id)
#
plt.figure(fignum+1)
plt.plot(rws['sweep_number'], rws['shear_init'], '.-', label='block_id: %d' % block_id)
plt.plot(rws['sweep_number'], rws['shear_final'], '.-', label='block_id: %d' % block_id)
plt.figure(fignum)
ax0.plot([min(self.shear_stress_sequences['sweep_number']), max(self.shear_stress_sequences['sweep_number'])], [0., 0.], 'k-')
ax0.legend(loc=0, numpoints=1)
plt.figure(fignum)
plt.title('Block shear_stress sequences')
plt.xlabel('sweep number')
plt.ylabel('shear stress')
def VisualizeAlm(alm,figno=1,max_l=None):
""" Visualize a healpy a_lm vector """
lmax = hp.Alm.getlmax(f_lm.size)
l,m = hp.Alm.getlm(lmax)
mag = np.zeros([lmax+1,lmax+1])
phs = np.zeros([lmax+1,lmax+1])
mag[m,l] = np.abs(alm)
phs[m,l] = np.angle(alm)
cl = hp.alm2cl(alm)
# Decide the range of l to plot
if max_l != None:
max_l = (max_l if (max_l <= lmax) else lmax)
else:
max_l = lmax
print max_l
plt.figure(figno)
plt.clf()
plt.subplot(211)
plt.imshow(mag[0:max_l,0:max_l],interpolation='nearest',origin='lower')
plt.colorbar()
plt.subplot(212)
plt.imshow(phs[0:max_l,0:max_l],interpolation='nearest',origin='lower')
plt.colorbar()
# plt.subplot(313)
#plt.semilogy(cl[0:max_l])
return {'mag':mag,'phs':phs,'cl':cl}
def check_vpd_ks2_astrometry():
"""
Check the VPD and quiver plots for our KS2-extracted, re-transformed astrometry.
"""
catFile = workDir + '20.KS2_PMA/wd1_catalog.fits'
tab = atpy.Table(catFile)
good = (tab.xe_160 < 0.05) & (tab.ye_160 < 0.05) & \
(tab.xe_814 < 0.05) & (tab.ye_814 < 0.05) & \
(tab.me_814 < 0.05) & (tab.me_160 < 0.05)
tab2 = tab.where(good)
dx = (tab2.x_160 - tab2.x_814) * ast.scale['WFC'] * 1e3
dy = (tab2.y_160 - tab2.y_814) * ast.scale['WFC'] * 1e3
py.clf()
q = py.quiver(tab2.x_814, tab2.y_814, dx, dy, scale=5e2)
py.quiverkey(q, 0.95, 0.85, 5, '5 mas', color='red', labelcolor='red')
py.savefig(workDir + '20.KS2_PMA/vec_diffs_ks2_all.png')
py.clf()
py.plot(dy, dx, 'k.', ms=2)
lim = 30
py.axis([-lim, lim, -lim, lim])
py.xlabel('Y Proper Motion (mas)')
py.ylabel('X Proper Motion (mas)')
py.savefig(workDir + '20.KS2_PMA/vpd_ks2_all.png')
idx = np.where((np.abs(dx) < 10) & (np.abs(dy) < 10))[0]
print('Cluster Members (within dx < 10 mas and dy < 10 mas)')
print((' dx = {dx:6.2f} +/- {dxe:6.2f} mas'.format(dx=dx[idx].mean(),
dxe=dx[idx].std())))
print((' dy = {dy:6.2f} +/- {dye:6.2f} mas'.format(dy=dy[idx].mean(),
dye=dy[idx].std())))
def window_fn_matrix(Q,N,num_remov=None,save_tag=None,lms=None):
Q = n.matrix(Q); N = n.matrix(N)
Ninv = uf.pseudo_inverse(N,num_remov=None) # XXX want to remove dynamically
#print Ninv
info = n.dot(Q.H,n.dot(Ninv,Q))
M = uf.pseudo_inverse(info,num_remov=num_remov)
W = n.dot(M,info)
if save_tag!=None:
foo = W[0,:]
foo = n.real(n.array(foo))
foo.shape = (foo.shape[1]),
print foo.shape
p.scatter(lms[:,0],foo,c=lms[:,1],cmap=mpl.cm.PiYG,s=50)
p.xlabel('l (color is m)')
p.ylabel('W_0,lm')
p.title('First Row of Window Function Matrix')
p.colorbar()
p.savefig('{0}/{1}_W.pdf'.format(fig_loc,save_tag))
p.clf()
print 'W ',W.shape
p.imshow(n.real(W))
p.title('Window Function Matrix')
p.colorbar()
p.savefig('{0}/{1}_W_im.pdf'.format(fig_loc,save_tag))
p.clf()
return W
def test_draw_xy_plot(self):
"""draw_xy_plot() properly produces an output html file
"""
out_file = os.path.join(self.dir_name, "test.html")
argv = (
"p.plot -x x -y btrace ctrace -s o- --xlabel myxlabel "
"--ylabel myylabel --title mytitle --theme darkgrid "
"--context talk --palette muted -a .5 --nogrid "
"--legend best --xlim 0 10 --ylim -10 10 "
"--savefig {}".format(out_file)
).split()
with patch("pandashells.lib.plot_lib.sys.argv", argv):
pl.clf()
df = pd.DataFrame({"x": range(10), "btrace": [-x for x in range(10)], "ctrace": [x for x in range(10)]})
parser = argparse.ArgumentParser()
arg_lib.add_args(parser, "io_in", "xy_plotting", "decorating", "example")
parser.add_argument("-a", "--alpha", help="Set opacity", nargs=1, default=[1.0], type=float)
args = parser.parse_args()
plot_lib.draw_xy_plot(args, df)
with open(out_file) as f:
html = f.read()
self.assertTrue("myxlabel" in html)
self.assertTrue("myylabel" in html)
self.assertTrue("mytitle" in html)
self.assertTrue("btrace" in html)
self.assertTrue("ctrace" in html)
self.assertTrue("1" in html)
self.assertTrue("10" in html)
def plotmodel(tractor, sig1, tt):
mod = tractor.getModelImage(0)
data = tractor.getImage(0).getImage()
noise = np.random.normal(size=data.shape) * sig1
imchi = dict(interpolation='nearest', origin='lower', cmap='RdBu',
vmin=-3, vmax=3)
plt.clf()
plt.subplot(2,2,1)
plt.imshow(data, **ima)
plt.title('Image')
plt.xticks([]); plt.yticks([])
plt.subplot(2,2,2)
plt.imshow(mod, **ima)
plt.title('Model')
plt.xticks([]); plt.yticks([])
plt.subplot(2,2,3)
plt.imshow(mod+noise, **ima)
plt.title('Model + noise')
plt.xticks([]); plt.yticks([])
plt.subplot(2,2,4)
# show mod - img to match "red-to-blue" colormap.
plt.imshow(-(data - mod)/sig1, **imchi)
plt.xticks([]); plt.yticks([])
plt.title('Chi')
plt.suptitle(tt)
ps.savefig()
def plotslice(pos,filename='',boxsize=100.):
ng = pos.shape[0]
M.clf()
M.scatter(pos[ng/4,:,:,1].flatten(),pos[ng/4,:,:,2].flatten(),s=1.,lw=0.)
M.axis('tight')
if filename != '':
M.savefig(filename)
def update(self):
if self.pose != []:
plt.figure(1)
clf()
self.fig1 = plt.figure(num=1, figsize=(self.window_size, \
self.window_size), dpi=80, facecolor='w', edgecolor='w')
title (self.title)
xlabel('Easting [m]')
ylabel('Northing [m]')
axis('equal')
grid (True)
poseT = zip(*self.pose)
pose_plt = plot(poseT[1],poseT[2],'#ff0000')
if self.wptnav != []:
mode = self.wptnav[-1][MODE]
if not (self.wptnav[-1][B_E] == 0 and self.wptnav[-1][B_N] == 0 and self.wptnav[-1][A_E] == 0 and self.wptnav[-1][A_N] == 0):
b_dot = plot(self.wptnav[-1][B_E],self.wptnav[-1][B_N],'ro',markersize=8)
a_dot = plot(self.wptnav[-1][A_E],self.wptnav[-1][A_N],'go',markersize=8)
ab_line = plot([self.wptnav[-1][B_E],self.wptnav[-1][A_E]],[self.wptnav[-1][B_N],self.wptnav[-1][A_N]],'g')
target_dot = plot(self.wptnav[-1][TARGET_E],self.wptnav[-1][TARGET_N],'ro',markersize=5)
if mode == -1:
pose_dot = plot(self.wptnav[-1][POSE_E],self.wptnav[-1][POSE_N],'b^',markersize=8)
elif mode == 1:
pose_dot = plot(self.wptnav[-1][POSE_E],self.wptnav[-1][POSE_N],'bs',markersize=8)
elif mode == 2:
pose_dot = plot(self.wptnav[-1][POSE_E],self.wptnav[-1][POSE_N],'bo',markersize=8)
if self.save_images:
self.fig1.savefig ('plot_map%05d.jpg' % self.image_count)
self.image_count += 1
draw()
def test_path(): "generate and draw a random path" path = genpath() P.ion() P.clf() draw_path(P.gca(), path) P.draw()
def do_Plot_item_a(Ustar, U, grad_phi):
""" plotting stuff: here we plot the first row with Ustar and
the second rows with Ud and grad phi, to see how they sum up """
pylab.clf()
pylab.cla()
f = pylab.figure()
f.text(.5, .95, r"Top: $U = U_d + \nabla \phi$, where " r"$U_d$ = - $\sin^2 ( \pi x)\sin(2 \pi y)\hat x$ + $\sin^2(\pi y)\sin(2\pi x)\hat y$ and $\phi = \frac{1}{10} \cos(2\pi y) \cos(2\pi x$) ", horizontalalignment='center', size=9)
pylab.subplot(221)
pylab.imshow(Ustar[0])
pylab.xlabel("Vector "r"$U_d$ in $\hat x$:" ,size=8)
pylab.ylabel("U in terms of # of cells in " r"$\hat x$", size=8)
pylab.subplot(222)
pylab.imshow(Ustar[1])
pylab.xlabel(r"Vector $\nabla \phi$ in $ \hat x $:", size=8)
pylab.ylabel("U in terms of # of cells in " r"$\hat y$",size=8)
pylab.subplot(223)
pylab.imshow(U [0])
pylab.ylabel("# of cells",size=8)
pylab.xlabel("# of cells",size=8)
pylab.subplot(224)
pylab.imshow(grad_phi [0])
pylab.xlabel("# of cells",size=8)
pylab.ylabel("# of cells",size=8)
pylab.savefig("plots/item_a_Ustar.png")
return 0
def __call__(self, n):
if len(self.f.shape) == 3:
# f = f[x,v,t], 2 dim in phase space
ft = self.f[n,:,:]
pylab.pcolormesh(self.X, self.V, ft.T, cmap = 'jet')
pylab.colorbar()
pylab.clim(0,0.38) # for Landau test case
pylab.grid()
pylab.axis([self.xmin, self.xmax, self.ymin, self.ymax])
pylab.xlabel('$x$', fontsize = 18)
pylab.ylabel('$v$', fontsize = 18)
pylab.title('$N_x$ = %d, $N_v$ = %d, $t$ = %2.1f' % (self.x.N, self.v.N, self.it*self.t.width))
pylab.savefig(self.path + self.filename)
pylab.clf()
return None
if len(self.f.shape) == 2:
# f = f[x], 1 dim in phase space
ft = self.f[n,:]
pylab.plot(self.x.gridvalues,ft,'ob')
pylab.grid()
pylab.axis([self.xmin, self.xmax, self.ymin, self.ymax])
pylab.xlabel('$x$', fontsize = 18)
pylab.ylabel('$f(x)$', fontsize = 18)
pylab.savefig(self.path + self.filename)
return None
def show(self,filename=None):
self.fig = fig = P.figure(self.fignum,self.figsize)
P.clf()
header = self.maps[0].header
self.grid = grid = ImageGrid(fig, (1, 1, 1),
nrows_ncols = (self.nrows, self.ncols),
share_all=True,
axes_class=(pywcsgrid2.Axes,
dict(header=header)),
**self.grid_kwargs)
for i,(map,lower,upper) in enumerate(zip(self.maps,self.lower_energies,self.upper_energies)):
map.show(axes=grid[i], cax=grid[i].cax)
format_energy=lambda x: '%.1f' % (x/1000.) if x < 1000 else '%.0f' % (x/1000.)
lower_string=format_energy(lower)
upper_string=format_energy(upper)
grid[i].add_inner_title("%s-%s GeV" % (lower_string,upper_string), loc=2)
if self.title is not None:
fig.suptitle(self.title)
tight_layout(fig)
if filename is not None: P.savefig(filename)
def plot_ch():
for job in jobs_orig:
print "plane of", job.path
pylab.clf()
x_center = int((job.position(0)[0] + job.position(1)[0])/2)
x_final = 50 + x_center
#plane = np.concatenate((job.plane(y=50)[:, x_final:],
# job.plane(y=50)[:, :x_final]), axis=1)
plane = job.plane(y=50)
myplane = plane[plane < 0.0]
p0 = myplane.min()
p12 = np.median(myplane)
p14 = np.median(myplane[myplane<p12])
p34 = np.median(myplane[myplane>p12])
p1 = myplane.max()
contour_values = (p0, p14, p12, p34, p1)
pylab.title(r'$u_x=%.4f,\ D_{-}=%.4f,\ D_{+}=%.4f,\ ch=%i$ ' %
(job.u_x, job.D_minus, job.D_plus, job.ch_objects))
car = pylab.imshow(plane, vmin=-0.001, vmax=0.0,
interpolation='nearest')
pylab.contour(plane, contour_values, linestyles='dashed',
colors='white')
pylab.grid(True)
pylab.colorbar(car)
#imgfilename = 'plane_r20-y50-u_x%.4fD%.4fch%03i.png' % \
# (job.u_x, job.D_minus, job.ch_objects)
imgfilename = 'plane_%s.png' % job.job_id
pylab.savefig(imgfilename)
def imshow_box(f,im, x,y,s):
'''imshow_box(f,im, x,y,s)
f: figure
im: image
x: center coordinate for box
y: center coord
s: box shape, (width, height)
'''
global coord
P.figure(f.number)
P.clf();
P.imshow(im);
P.axhline(y-s[1]/2.)
P.axhline(y+s[1]/2.)
P.axvline(x-s[0]/2.)
P.axvline(x+s[0]/2.)
xy=crop(m,s,y,x)
coord=(0.5*(xy[2]+xy[3]), 0.5*(xy[0]+xy[1]))
P.title(str('x: %d y: %d' % (x,y)));
P.figure(999);
P.imshow(master[xy[0]:xy[1],xy[2]:xy[3]])
P.title('Master');
P.figure(998);
df=(master[xy[0]:xy[1],xy[2]:xy[3]]-slave)
P.imshow(np.abs(df))
P.title(str('RMS: %0.6f' % np.sqrt((df**2.).mean()) ));
def savepng(pre, img, title=None, **kwargs):
fn = '%s-%s.png' % (pre, idstr)
print 'Saving', fn
plt.clf()
plt.imshow(img, **kwargs)
ax = plt.axis()
if debug:
print len(xplotx),len(allobjx)
for i,(objx,objy,objc) in enumerate(zip(allobjx,allobjy,allobjc)):
plt.plot(objx,objy,'-',c=objc)
tempx = []
tempx.append(xplotx[i])
tempx.append(objx[0])
tempy = []
tempy.append(xploty[i])
tempy.append(objy[0])
plt.plot(tempx,tempy,'-',c='purple')
plt.plot(pointx,pointy,'y.')
plt.plot(xplotx,xploty,'xg')
plt.axis(ax)
if title is not None:
plt.title(title)
plt.colorbar()
plt.gray()
plt.savefig(fn)
def clicker2(event):
global mask, aid, bid, cid, did, eid, fid, done
if event.inaxes:
if event.button == 1:
if (event.x > 601 and event.x < 801 and
event.y > 422 and event.y < 482):
disconnect(aid)
disconnect(bid)
disconnect(cid)
disconnect(did)
disconnect(eid)
disconnect(fid)
try:
lines, status = kepio.openascii(maskfile,'r',None,False)
for line in lines:
mask = []
work = line.strip().split('|')
y0 = int(work[3])
x0 = int(work[4])
work = work[5].split(';')
for i in range(len(work)):
y = int(work[i].split(',')[0]) + y0
x = int(work[i].split(',')[1]) + x0
mask.append(str(x) + ',' + str(y))
pylab.clf()
plotimage(cmdLine)
except:
txt = 'ERROR -- KEPMASK: Cannot open or read mask file ' + maskfile
kepmsg.err(logfile,txt,True)
return
def draw(self):
print self.edgeno
pos = 0
dy = 8
edgeno = self.edgeno
edge = self.edges[edgeno]
edgeprev = self.edges[edgeno-1]
p = np.round(edge["top"](1024))
top = min(p+2*dy, 2048)
bot = min(p-2*dy, 2048)
self.cutout = self.flat[1][bot:top,:].copy()
pl.figure(1)
pl.clf()
start = 0
dy = 512
for i in xrange(2048/dy):
pl.subplot(2048/dy,1,i+1)
pl.xlim(start, start+dy)
if i == 0: pl.title("edge %i] %s|%s" % (edgeno,
edgeprev["Target_Name"], edge["Target_Name"]))
pl.subplots_adjust(left=.07,right=.99,bottom=.05,top=.95)
pl.imshow(self.flat[1][bot:top,start:start+dy], extent=(start,
start+dy, bot, top), cmap='Greys', vmin=2000, vmax=6000)
pix = np.arange(start, start+dy)
pl.plot(pix, edge["top"](pix), 'r', linewidth=1)
pl.plot(pix, edgeprev["bottom"](pix), 'r', linewidth=1)
pl.plot(edge["xposs_top"], edge["yposs_top"], 'o')
pl.plot(edgeprev["xposs_bot"], edgeprev["yposs_bot"], 'o')
hpp = edge["hpps"]
pl.axvline(hpp[0],ymax=.5, color='blue', linewidth=5)
pl.axvline(hpp[1],ymax=.5, color='red', linewidth=5)
hpp = edgeprev["hpps"]
pl.axvline(hpp[0],ymin=.5,color='blue', linewidth=5)
pl.axvline(hpp[1],ymin=.5,color='red', linewidth=5)
if False:
L = top-bot
Lx = len(edge["xposs"])
for i in xrange(Lx):
xp = edge["xposs"][i]
frac1 = (edge["top"](xp)-bot-1)/L
pl.axvline(xp,ymin=frac1)
for xp in edgeprev["xposs"]:
frac2 = (edgeprev["bottom"](xp)-bot)/L
pl.axvline(xp,ymax=frac2)
start += dy
def displayRetirementWithMonthlies(monthlies, rate, terms):
plt.figure('retireMonth')
plt.clf()
for monthly in monthlies:
xvals, yvals = retire(monthly, rate, terms)
plt.plot(xvals, yvals, label = 'retire:'+str(monthly))
plt.legend(loc = 'upper left')
def plot_item(self, m, ind, x, r, k, label):
"""plot_item(self, m, ind, x, r, k, label)
Plot selection m (index ind, data in x) and its reconstruction r,
with k and label to annotate of the plot.
"""
if x == [] or r == []:
print "Error: No data in x and/or r."
return
pylab.clf()
# xvals, x, and r need to be column vectors
pylab.plot(self.xvals, r, color='0.6', label='Expected')
# Color code:
# positive residuals = red
# negative residuals = blue
pylab.plot(self.xvals, x, color='0.0', label='Observed')
posres = np.where((x-r) > 0)[0]
negres = np.where((x-r) < 0)[0]
pylab.plot(self.xvals[posres], x[posres], 'r.', markersize=3, label='Higher')
pylab.plot(self.xvals[negres], x[negres], 'b.', markersize=3, label='Lower')
pylab.xlabel(self.xlabel)
pylab.ylabel(self.ylabel)
pylab.title('DEMUD selection %d (%s), item %d, using K=%d' % \
(m, label, ind, k))
pylab.legend() #fontsize=10)
outdir = os.path.join('results', self.name)
if not os.path.exists(outdir):
os.mkdir(outdir)
figfile = os.path.join(outdir, 'sel-%d-k-%d-(%s).png' % (m, k, label))
pylab.savefig(figfile)
print 'Wrote plot to %s' % figfile
def compute_parameters(input_data):
"""
Build the required HTML response to be displayed.
"""
figure = pylab.figure(figsize=(7, 8))
pylab.clf()
matrix = input_data.ordered_weights
matrix_size = input_data.number_of_regions
labels = input_data.ordered_labels
plot_title = "Connection Strength"
order = numpy.arange(matrix_size)
# Assumes order is shape (number_of_regions, )
order_rows = order[:, numpy.newaxis]
order_columns = order_rows.T
axes = figure.gca()
img = axes.matshow(matrix[order_rows, order_columns])
axes.set_title(plot_title)
figure.colorbar(img)
if labels is None:
return
axes.set_yticks(numpy.arange(matrix_size))
axes.set_yticklabels(list(labels[order]), fontsize=8)
axes.set_xticks(numpy.arange(matrix_size))
axes.set_xticklabels(list(labels[order]), fontsize=8, rotation=90)
figure.canvas.draw()
parameters = dict(mplh5ServerURL=TvbProfile.current.web.MPLH5_SERVER_URL,
figureNumber=figure.number, showFullToolbar=False)
return parameters, {}
def EBTransitPhase(tset, kid_x):
ebp = atpy.Table('%s/eb_pars.txt' %dir, type = 'ascii')
lc = tset.tables[1]
time = lc.TIME
flux = lc.PDCSAP_FLUX
nobs = len(time)
lg = scipy.isfinite(time)
pylab.figure(52)
pylab.clf()
pylab.plot(time[lg], flux[lg])
npl = 2
phase = scipy.zeros((npl, nobs))
inTr = scipy.zeros((npl, nobs), 'int')
period = ebp.P[ebp.KID == kid_x]
for ipl in scipy.arange(npl):
if ipl == 0: t0 = ebp.Ep1[ebp.KID == kid_x]
if ipl == 1: t0 = ebp.Ep2[ebp.KID == kid_x]
if ipl == 0: dur = ebp.Dur1[ebp.KID == kid_x]
if ipl == 1: dur = ebp.Dur2[ebp.KID == kid_x]
dur /= period
counter = 0
while (time[lg] - t0).min() < 0:
t0 -= period
counter += 1
if counter > 1000: break
ph = ((time - t0) % period) / period
ph[ph < -0.5] += 1
ph[ph > 0.5] -= 1
phase[ipl,:] = ph
inTr[ipl,:] = (abs(ph) <= dur/1.5)
return phase, inTr
def dovis(self):
"""
Do runtime visualization.
"""
pylab.clf()
phi = self.cc_data.get_var("phi")
myg = self.cc_data.grid
pylab.imshow(numpy.transpose(phi[myg.ilo:myg.ihi+1,
myg.jlo:myg.jhi+1]),
interpolation="nearest", origin="lower",
extent=[myg.xmin, myg.xmax, myg.ymin, myg.ymax])
pylab.xlabel("x")
pylab.ylabel("y")
pylab.title("phi")
pylab.colorbar()
pylab.figtext(0.05,0.0125, "t = %10.5f" % self.cc_data.t)
pylab.draw()
def field_map_ndar(ndar_field,t,ar_coorx,ar_coory,X,image_out,variable):
ar_field=ndar_field[t,:]
max_val=int(np.max(ndar_field))
if variable==4:
max_val=100.
xmin=min(ar_coorx);xmax=max(ar_coorx)
ymin=min(ar_coory);ymax=max(ar_coory)
step=X
nx=(xmax-xmin)/step+1
ny=(ymax-ymin)/step+1
ar_indx=np.array((ar_coorx-xmin)/step,int)
ar_indy=np.array((ar_coory-ymin)/step,int)
ar_map=np.ones((ny,nx))*-99.9
ar_map[ar_indy,ar_indx]=ar_field
ar_map2 = M.masked_where(ar_map <0, ar_map)
ut.check_file_exist(image_out)
pl.clf()
pl.axes(axisbg='gray')
pl.imshow(ar_map2, cmap=pl.cm.RdBu,
interpolation='Nearest', origin='lower', vmax=max_val, vmin=0)
pl.title('time step= '+ut.string(t,len(str(t))))
pl.colorbar()
pl.savefig(image_out)
def plot_vector_diff_F160W():
"""
Using the xym2mat analysis on the F160W filter in the 2010 data set,
plot up the positional offset vectors for each reference star in
each star list relative to the average list. This should show
us if there are systematic problems with the distortion solution
or PSF variations.
"""
x, y, m, xe, ye, me, cnt = load_catalog()
dx = x - x[0]
dy = y - y[0]
dr = np.hypot(dx, dy)
py.clf()
py.subplots_adjust(left=0.05, bottom=0.05, right=0.95, top=0.95)
for ii in range(1, x.shape[0]):
idx = np.where((x[ii,:] != 0) & (y[ii,:] != 0) & (dr[ii,:] < 0.1) &
(xe < 0.05) & (ye < 0.05))[0]
py.clf()
q = py.quiver(x[0,idx], y[0,idx], dx[ii, idx], dy[ii, idx], scale=1.0)
py.quiverkey(q, 0.9, 0.9, 0.03333, label='2 mas', color='red')
py.title('{0} stars in list {1}'.format(len(idx), ii))
py.xlim(0, 4500)
py.ylim(0, 4500)
foo = input('Continue?')
if foo == 'q' or foo == 'Q':
break
def plot_mcmc_results(chain):
# Pull m and b arrays out of the Markov chain.
mm = [m for b,m in chain]
bb = [b for b,m in chain]
# Scatterplot of m,b posterior samples
plt.clf()
plt.contour(bgrid, mgrid, posterior, pdf_contour_levels(posterior))
plt.plot(bb, mm, 'b.', alpha=0.1)
plot_mb_setup()
plt.show()
# Histograms
import triangle
triangle.corner(chain, labels=['b','m'], extents=[0.99]*2)
plt.show()
# Traces
plt.clf()
plt.subplot(2,1,1)
plt.plot(mm, 'k-')
plt.ylim(mlo,mhi)
plt.ylabel('m')
plt.subplot(2,1,2)
plt.plot(bb, 'k-')
plt.ylabel('b')
plt.ylim(blo,bhi)
plt.show()
def newFigLayer():
pylab.clf()
pylab.figure(figsize=(8, 8))
pylab.axes([0.15, 0.15, 0.8, 0.81])
pylab.axis([0.6, -0.4, -0.4, 0.6])
pylab.xlabel(r"$\Delta$\textsf{RA from Sgr A* (arcsec)}")
pylab.ylabel(r"$\Delta$\textsf{Dec. from Sgr A* (arcsec)}")
def test_pixpsf(self):
tim,tinf = get_tractor_image_dr8(94, 2, 520, 'i', psf='kl-pix',
roi=[500,600,500,600], nanomaggies=True)
psf = tim.getPsf()
print 'PSF', psf
for i,(dx,dy) in enumerate([
(0.,0.), (0.2,0.), (0.4,0), (0.6,0),
(0., -0.2), (0., -0.4), (0., -0.6)]):
px,py = 50.+dx, 50.+dy
patch = psf.getPointSourcePatch(px, py)
print 'Patch size:', patch.shape
print 'x0,y0', patch.x0, patch.y0
H,W = patch.shape
XX,YY = np.meshgrid(np.arange(W), np.arange(H))
im = patch.getImage()
cx = patch.x0 + (XX * im).sum() / im.sum()
cy = patch.y0 + (YY * im).sum() / im.sum()
print 'cx,cy', cx,cy
print 'px,py', px,py
self.assertLess(np.abs(cx - px), 0.1)
self.assertLess(np.abs(cy - py), 0.1)
plt.clf()
plt.imshow(patch.getImage(), interpolation='nearest', origin='lower')
plt.title('dx,dy %f, %f' % (dx,dy))
plt.savefig('pixpsf-%i.png' % i)
def graphTSPResults(resultsDir,numberOfTours):
x=[]
y=[]
files=[open("%s/objectiveFunctionReport.txt" % resultsDir),
open("%s/fitnessReport.txt" % resultsDir)]
for f in files:
x.append([])
y.append([])
i=len(x)-1
for line in f:
line=line.split(',')
if line[0] != "gen":
x[i].append(int(line[0]))
y[i].append(float(line[1] if i==1 else line[2]))
ylen=len(y[0])
pl.subplot(2,1,1)
pl.plot(x[0],y[0],'bo')
pl.ylabel('Minimum Distance')
pl.title("TSP with a %s City Tour" % numberOfTours)
pl.annotate("{0:,}".format(y[0][0]),xy=(x[0][0],y[0][0]), xycoords='data',
xytext=(30, -30), textcoords='offset points',
arrowprops=dict(arrowstyle="->") )
pl.annotate("{0:,}".format(y[0][ylen-1]),xy=(x[0][ylen-1],y[0][ylen-1]), xycoords='data',
xytext=(-30,30), textcoords='offset points',
arrowprops=dict(arrowstyle="->") )
pl.subplot(2,1,2)
pl.plot(x[1],y[1],'go')
pl.xlabel('Generation')
pl.ylabel('Fitness')
pl.savefig("%s/tsp_result.png" % resultsDir)
pl.clf()
def find_edge_pair(data, y, roi_width, edgeThreshold=450):
'''
find_edge_pair finds the edge of a slit pair in a flat
data[2048x2048]: a well illuminated flat field [DN]
y: guess of slit edge position [pix]
Keywords:
edgeThreshold: the pixel value below which we should ignore using
to calculate edges.
Moves along the edge of a slit image
- At each location along the slit edge, determines
the position of the demarcations between two slits
Outputs:
xposs []: Array of x positions along the slit edge [pix]
yposs []: The fitted y positions of the "top" edge of the slit [pix]
widths []: The fitted delta from the top edge of the bottom [pix]
scatters []: The amount of light between slits
The procedure is as follows
1: starting from a guess spatial position (parameter y), march
along the spectral direction in some chunk of pixels
2: At each spectral location, construct a cross cut across the
spatial direction; select_roi is used for this.
3: Fit a two-sided error function Fit.residual_disjoint_pair
on the vertical cross cut derived in step 2.
4: If the fit fails, store it in the missing list
- else if the top fit is good, store the top values in top vector
- else if the bottom fit is good, store the bottom values in bottom
vector.
5: In the vertical cross-cut, there is a minimum value. This minimum
value is stored as a measure of scattered light.
Another procedure is used to fit polynomials to these fitted values.
'''
def select_roi(data, roi_width):
v = data[y-roi_width:y+roi_width, xp-2:xp+2]
v = np.median(v, axis=1) # Axis = 1 is spatial direction
return v
xposs_top = []
yposs_top = []
xposs_top_missing = []
xposs_bot = []
yposs_bot = []
xposs_bot_missing = []
yposs_bot_scatters = []
#1
rng = np.linspace(10, 2040, 50).astype(np.int)
for i in rng:
xp = i
#2
v = select_roi(data, roi_width)
xs = np.arange(len(v))
# Modified from 450 as the hard coded threshold to one that
# can be controlled by a keyword
if (np.median(v) < edgeThreshold):
xposs_top_missing.append(xp)
xposs_bot_missing.append(xp)
continue
#3
ff = Fit.do_fit(v, residual_fun=Fit.residual_disjoint_pair)
fit_ok = 0 < ff[4] < 4
if fit_ok:
(sigma, offset, mult1, mult2, add, width) = ff[0]
xposs_top.append(xp)
yposs_top.append(y - roi_width + offset + width)
xposs_bot.append(xp)
yposs_bot.append(y - roi_width + offset)
between = offset + width/2
if 0 < between < len(v)-1:
start = np.max([0, between-2])
stop = np.min([len(v),between+2])
yposs_bot_scatters.append(np.min(v[start:stop])) # 5
if False:
pl.figure(2)
pl.clf()
tmppix = np.arange(y-roi_width, y+roi_width)
tmpx = np.arange(len(v))
pl.axvline(y - roi_width + offset + width, color='red')
pl.axvline(y - roi_width + offset, color='red')
pl.scatter(tmppix, v)
pl.plot(tmppix, Fit.fit_disjoint_pair(ff[0], tmpx))
pl.axhline(yposs_bot_scatters[-1])
pl.draw()
else:
yposs_bot_scatters.append(np.nan)
else:
xposs_bot_missing.append(xp)
xposs_top_missing.append(xp)
info("Skipping wavelength pixel): %i" % (xp))
return map(np.array, (xposs_bot, xposs_bot_missing, yposs_bot, xposs_top,
xposs_top_missing, yposs_top, yposs_bot_scatters))
def plot_cmd(allmags, i2mags, band, catflags, classstar):
print('i2 mags shape', i2mags.shape)
print('allmags shape', allmags.shape)
print('catflags shape', catflags.shape)
plt.figure(figsize=(6, 6))
plt.clf()
#plotpos0 = [0.15, 0.15, 0.84, 0.80]
#plt.gca().set_position(plotpos0)
xx, yy, xerr = [], [], []
xx2, xerr2 = [], []
for i2, rr in zip(i2mags, allmags):
#print 'rr', rr
# When the source is off the image, the optimizer doesn't change anything and
# we end up with r = i2
I = (rr != i2)
rr = rr[I]
ii2 = i2.repeat(len(rr))
rr = np.minimum(rr, 25.)
#plt.plot(rr - ii2, ii2, 'o', mfc='b', mec='none', ms=5, alpha=0.5)
mr = np.mean(rr)
sr = np.std(rr)
#plt.plot([(mr-sr) - i2, (mr+sr) - i2], [i2,i2], 'b-', lw=3, alpha=0.25)
medr = np.median(rr)
iqr = (1. / 0.6745) * 0.5 * (np.percentile(rr, 75) -
np.percentile(rr, 25))
#plt.plot([(medr - iqr) - i2, (medr + iqr) - i2], [i2,i2], 'g-', lw=3, alpha=0.25)
xx.append(mr - i2)
yy.append(i2)
xerr.append(sr)
xx2.append(medr - i2)
xerr2.append(iqr)
yy2 = np.array(yy)
xx2 = np.array(xx2)
xerr2 = np.array(xerr2)
I = (xerr2 < 1)
xx2 = xx2[I]
yy2 = yy2[I]
xerr2 = xerr2[I]
flag = catflags[I]
cstar = classstar[I]
plt.clf()
#plt.plot(xx2, yy2, 'o', mfc='b', mec='none', mew=0, ms=5, alpha=0.8)
LL = []
for F, c in [((flag > 0), '0.5'), ((flag == 0) * (cstar < 0.5), 'b'),
((flag == 0) * (cstar >= 0.5), 'g')]:
p1 = plt.plot(xx2[F],
yy2[F],
'o',
mfc=c,
mec='none',
mew=0,
ms=5,
alpha=0.8)
LL.append(p1[0])
plt.plot([xx2[F] - xerr2[F], xx2[F] + xerr2[F]], [yy2[F], yy2[F]],
'-',
color=c,
lw=2,
mew='none',
alpha=0.5)
#plt.axis([-3, 3, 21.5, 15.5])
plt.legend(LL, ('flagged', 'galaxy', 'star'))
plt.ylim(21.5, 15.5)
cl, ch = {
'u': (-3, 6),
'g': (-1, 5),
'r': (-2, 3),
'i': (-2, 2),
'z': (-2, 1),
'w1': (-10, 10),
'w2': (-10, 10),
'w3': (-10, 10),
'w4': (-10, 10),
}[band]
plt.xticks(range(cl, ch + 1))
plt.xlim(cl, ch)
plt.xlabel('SDSS %s - CFHT i (mag)' % band)
plt.ylabel('CFHT i (mag)')
plt.yticks(range(16, 21 + 1))
plt.title('CS82 test patch: SDSS--CFHT CMD')
plt.savefig('cmd-%s.png' % band)
plt.savefig('cmd-%s.pdf' % band)
I = np.flatnonzero((flag == 0) * (xx2 < -1))
print('Not-flagged and c < -1:', I)
return I
mn1, mn2 = [], []
for i, (s1, s2) in enumerate(zip(m1.T, m2.T)):
print('src', i)
print('i2mag', i2mags[i])
print('mag 1', s1)
print('mag 2', s2)
s1 = s1[np.isfinite(s1)]
s2 = s2[np.isfinite(s2)]
if len(s1) == 0 or len(s2) == 0:
continue
mn1.append(np.median(s1))
mn2.append(np.median(s2))
mn1 = np.array(mn1)
mn2 = np.array(mn2)
plt.clf()
#I = np.flatnonzero(np.isfinite(m1) * np.isfinite(m2))
#if len(I) == 0:
# print 'No', b1, 'and', b2, 'mags'
# continue
#plt.plot(m1[I], m1[I]-m2[I], 'k.')
plt.plot(mn1, mn1 - mn2, 'k.')
plt.xlabel('band ' + b1)
plt.ylabel('band %s - %s' % (b1, b2))
plt.savefig('cmd-%s-%s.png' % (b1, b2))
from cs82 import *
RA = 334.32
DEC = 0.315
sz = 0.12 * 3600.
pixscale = 0.187
def generateFigsAndDatafiles(self,
overwrite,
outdir=None,
begin=None,
includeraw=True,
grid=False):
"""
Our plots will start at time=begin (in nanoseconds). If begin is set to None,
we will just start at the beginning of the data.
"""
cols = 4
if outdir is None:
outdir = os.path.join(self.directory, 'props')
datadir = os.path.join(outdir, 'data')
if not overwrite:
if os.path.exists(outdir):
sys.exit(
'Output directory (%s) exists. Please remove it or set "overwrite" to True.'
% outdir)
os.system('mkdir -p ' + datadir)
propnames = []
# We use a different definition of this funciton below to get relative links in the HTML file.
def figname(pn):
return os.path.join(datadir, pn + '.png')
def dataname(pn):
return os.path.join(datadir, pn + '.dat')
def savedata(p, fname):
d = self._props[p]
x = d[:, 0]
# convert ps to ns
x = x / 1000.
y = d[:, 1]
f = file(fname, 'w')
for xy in zip(x, y):
f.write('%f\t%f\n' % xy)
f.close()
for p in self._props.keys():
pn = ''.join([
i for i in p
if i in 'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
])
print "Doing", p
clf()
if p in self._averprops:
if p.startswith(
'H'
) and False: # Hopefully dealt with by not plotting more than 200k points.
print "Trying to skip raw for", p
self.plotaver(p, begin=begin, includeraw=False, grid=grid)
else:
self.plotaver(p,
begin=begin,
includeraw=includeraw,
grid=grid)
else:
self.plotprop(p, begin=begin, grid=grid)
### Note: This call to savefig often fails with the
### following runtime error:
### RuntimeError: Agg rendering complexity exceeded. Consider downsampling or decimating your data.
### when plotting HFCTote with raw data
### shown. Unfortunately, catching the error, calling clf,
### and replotting without the raw data produces exactly
### the same error. The only thing that seems to help is
### just setting includeraw to false the first time through.
### Hence the check for p.startswith('H') above. FWIW, I think
### I tried it with just checking for HFCTote, but that failed.
### I might have gotten the syntax wrong, though.
### It looks like I've fixed that completely by just
### plotting 200k points, but I've left the comments in
### for clarity.
savefig(figname(pn))
savedata(p, dataname(p))
propnames.append(pn)
html = '''<html><head><title>CHARMM Output Properties</title></head><body><h1>CHARMM Output Properties</h1><br><h2>Click on thumbnails for larger pictures</h2><br><table border="0" cellpadding="7" cellspacing="0">'''
def figname(pn):
return os.path.join('data', pn + '.png')
propnames.sort()
for tr in splitseq(propnames, cols):
html += '<tr>'
for td in tr:
html += ' <td>%s<br><a href="%s"><img src="%s" width="100%%"/></td>\n' % (
td, figname(td), figname(td))
html += '</tr>'
html += '</table></body></html>'
f = file(os.path.join(outdir, 'index.html'), 'w')
f.write(html)
f.close()
def _pp(self, clear, r, c, props):
if clear: clf()
for (i, p) in enumerate(props):
subplot(r, c, i + 1)
self.plotprop(p)
def plotdata(x,
y=None,
yerr=None,
numblocks=10,
numerrbars=50,
colors=('blue', 'green'),
clear=False,
plottitle=None,
xaxislabel=None,
yaxislabel=None,
description='',
grid=False):
""" Our standard plotting routine.
- The first argument is the data. We try to extract x and y data from it if possible.
- Plot 50 error bars if we're given errors.
- Do block averaging.
- description gets added to the legend and title.
"""
txt = ''
# Figure out x,y,err
if y is None:
if len(x.shape) > 1:
x, y = x[:, 0], x[:, 1]
else:
x, y = array(range(len(x))), x
if clear: clf()
if len(x) >= 100000:
step = divmod(len(x), 100000)[0]
else:
step = 1
plot(x[::step],
y[::step],
color=colors[0],
zorder=10,
alpha=0.5,
label=description + 'raw data')
xmin, xmax, ymin, ymax = x.min(), x.max(), y.min(), y.max()
#print y
if yerr is not None:
error_step = int(len(x) / numerrbars)
if error_step == 0: error_step = len(x)
errorbar(x[::error_step],
y[::error_step],
yerr[::error_step],
color=colors[0],
zorder=20,
label='FLUC>')
ymin = ymin - abs(yerr.max())
ymax = ymax + abs(yerr.max())
else:
ymin = ymin - abs(.1 * ymin)
ymax = ymax - abs(.1 * ymax)
if numblocks <= len(x):
blocksize = int(len(x) / numblocks)
else:
blocksize = 1
numblocks = len(x)
print "Not enough data points, setting blocksize to", blocksize, "and numblocks to", numblocks
blocksizes = [len(i) for i in splitseq(x, blocksize)]
x = [average(i) for i in splitseq(x, blocksize)][:numblocks]
yerr = array([std(i) for i in splitseq(y, blocksize)])[:numblocks]
y = array([average(i) for i in splitseq(y, blocksize)])[:numblocks]
txt += 'Avg: %.4f' % average(y)
txt += ', std err: %.4f, avg err: %.4f' % (std(y), average(yerr))
txt += '\nblocks of length %s' % blocksize
if len(blocksizes) > numblocks:
txt += ' discarding %s points at the end' % sum(blocksizes[numblocks:])
txt += '\nslope of best-fit line to block averages: %s' % u.fitline(x,
y)[0]
#print y
#errorbar(x,y,yerr,elinewidth=20,color=colors[1],barsabove=True,zorder=30)
errorbar(x,
y,
yerr,
color=colors[1],
barsabove=True,
zorder=30,
label=description + 'block averages')
# After the last plotting, we need to set the axis explicitly,
# due to the fact that someone might have previously plotted
# raw data in plotaver(). In that case, we still want to be
# zoomed in on the average data.
axis([xmin, xmax, ymin, ymax])
if plottitle: title(description + plottitle)
if xaxislabel: xlabel(xaxislabel)
if yaxislabel: ylabel(yaxislabel)
if grid: P.grid('on')
else: P.grid('off')
annotation_location = (min(x) + (max(x) - min(x)) * 0.1,
min(y) + (max(y) - min(y)) * 0.1)
annotation_location = (xmin + (xmax - xmin) * 0.1,
ymin + (ymax - ymin) * 0.1)
#print annotation_location,max(y)
annotate(txt, annotation_location)
legend(shadow=True)
def run(self):
if self.debug:
import pdb
pdb.set_trace()
db = Stock_250kDB.Stock_250kDB(drivername=self.drivername,
username=self.db_user,
password=self.db_passwd,
hostname=self.hostname,
database=self.dbname,
schema=self.schema)
db.setup(create_tables=False)
session = db.session
header_phen, strain_acc_list_phen, category_list_phen, data_matrix_phen = read_data(
self.phenotype_fname, turn_into_integer=0)
phenData = SNPData(
header=header_phen,
strain_acc_list=strain_acc_list_phen,
data_matrix=data_matrix_phen
) #row label is that of the SNP matrix, because the phenotype matrix is gonna be re-ordered in that way
phenData.data_matrix = Kruskal_Wallis.get_phenotype_matrix_in_data_matrix_order(
phenData.row_id_ls, strain_acc_list_phen,
phenData.data_matrix) #tricky, using strain_acc_list_phen
phenotype_col_index1 = self.findOutWhichPhenotypeColumn(
phenData, Set([self.phenotype_method_id1]))[0]
phenotype_col_index2 = self.findOutWhichPhenotypeColumn(
phenData, Set([self.phenotype_method_id2]))[0]
x_ls = []
y_ls = []
for i in range(phenData.data_matrix.shape[0]):
if not numpy.isnan(
phenData.data_matrix[i]
[phenotype_col_index1]) and not numpy.isnan(
phenData.data_matrix[i][phenotype_col_index2]):
x_ls.append(phenData.data_matrix[i][phenotype_col_index1])
y_ls.append(phenData.data_matrix[i][phenotype_col_index2])
pylab.clf()
pylab.title('Phenotype Contrast')
pylab.plot(x_ls, y_ls, '.', alpha=0.6)
pylab.grid(alpha=0.3)
phenotype_method1 = Stock_250kDB.PhenotypeMethod.get(
self.phenotype_method_id1)
phenotype_method2 = Stock_250kDB.PhenotypeMethod.get(
self.phenotype_method_id2)
pylab.xlabel(phenotype_method1.short_name)
pylab.ylabel(phenotype_method2.short_name)
#draw diagonal line to show perfect correlation
max_min_value = max(min(x_ls), min(y_ls))
min_max_value = min(max(x_ls), max(y_ls))
pylab.plot([max_min_value, min_max_value],
[max_min_value, min_max_value],
c='g',
alpha=0.7)
png_output_fname = '%s.png' % self.output_fname_prefix
pylab.savefig(png_output_fname, dpi=400)
pylab.savefig('%s.svg' % self.output_fname_prefix)
def klf_simulation():
"""
Plot up a simulated KLF for the young star cluster at the Galactic Center
and show spectroscopic and photometric detections today with Keck and in the
future with TMT.
"""
t = atpy.Table('/u/jlu/work/tmt/tmt_sim_klf_t6.78.txt', type='ascii')
nrowsOld = len(t)
# Chop off everything below 0.1 Msun since we don't have models there anyhow
t = t.where(t['Mass'] >= 0.1)
nrows = len(t)
print 'Found %d out of %d stars above 0.1 Msun' % (nrows, nrowsOld)
# Assign arbitrary magnitudes for WR stars. Uniformly distributed from Kp=9-12
idx = np.where(t['isWR'] == 'True')[0]
t['Kp'][idx] = 9.0 + (np.random.rand(len(idx)) * 3)
print t['Kp'][idx]
kbins = np.arange(9.0, 24, 0.5)
# Plot the KLF
py.clf()
py.hist(t['Kp'], bins=kbins, histtype='step', linewidth=2)
py.gca().set_yscale('log')
py.xlabel('Kp (d=8 kpc, AKs=2.7)')
py.ylabel('Number of Stars')
py.title('Galactic Center Young Cluster')
py.xlim(9, 23)
rng = py.axis()
py.plot([15, 15], [rng[2], rng[3]], 'k--', linewidth=2)
py.text(15.1, 4e4, r'13 M$_\odot$', horizontalalignment='left')
ar1 = FancyArrow(15,
10**3,
-1,
0,
width=10,
color='black',
head_length=0.3)
py.gca().add_patch(ar1)
py.text(14.8,
7e2,
'Keck\nSpectra',
horizontalalignment='right',
verticalalignment='top')
py.plot([20, 20], [rng[2], rng[3]], 'k-', linewidth=2)
py.text(20.1, 4e4, r'0.5 M$_\odot$', horizontalalignment='left')
ar1 = FancyArrow(20, 3e4, -1, 0, width=300, color='black', head_length=0.3)
py.gca().add_patch(ar1)
py.text(19.8,
2.2e4,
'TMT\nSpectra',
horizontalalignment='right',
verticalalignment='top')
ar1 = FancyArrow(18.2, 10, 0, 13, width=0.1, color='blue', head_length=10)
py.gca().add_patch(ar1)
py.text(18,
9,
'Pre-MS\nTurn-On',
color='blue',
horizontalalignment='center',
verticalalignment='top')
py.savefig('/u/jlu/work/tmt/gc_klf_spectral_sensitivity.png')
def runOptimization(self, id_to_name_nodemap, name_to_id_nodemap, max_stations):
print '\nRunning Optimization with:'
print '\tMAX BOOSTERS = ', max_stations
solve_timelimit = None
p = (1,"There was a problem with the 'model type' or 'model format' options")
cmd = None
Solution = {}
Solution['detected scenarios'] = {}
if self.getBoosterOption('model format') == 'AMPL':
exe = self.getConfigureOption('ampl executable')
inp = os.path.join(os.path.abspath(os.curdir),self.getConfigureOption('output prefix')+'-ampl-b'+str(max_stations)+'.run')
out = os.path.join(os.path.abspath(os.curdir),self.getConfigureOption('output prefix')+'-ampl-b'+str(max_stations)+'.out')
results_file, concentrations_file, mass_injections_file = self.createAmplRun(name_to_id_nodemap, max_stations, inp)
cmd = '%s %s'%(exe,inp)
# Delete the possibly existing results file with the same name before-hand,
# that way we'll know if AMPL failed
try:
os.remove(results_file)
except OSError:
# the file did not exist
pass
try:
os.remove(concentrations_file)
except OSError:
# the file did not exist
pass
try:
os.remove(mass_injections_file)
except OSError:
# the file did not exist
pass
print 'Launching AMPL ...'
p = pyutilib.subprocess.run(cmd,timelimit=solve_timelimit,outfile=out)
if (p[0] or not os.path.isfile(results_file)):
print >> sys.stderr, '\nAn error occured when running the optimization problem'
print >> sys.stderr, 'Error Message: ', p[1]
print >> sys.stderr, 'Command: ', cmd, '\n'
raise RuntimeWarning('Optimization Failed')
#try to load the results file
f = open(results_file,'r')
ampl_sol = yaml.load(f)
f.close()
if (ampl_sol['solve_result_num'] >= 100) or (ampl_sol['solve_result'] != 'solved') or (ampl_sol['solve_exitcode'] != 0):
print >> sys.stderr, ' '
print >> sys.stderr, 'WARNING: AMPL solver statuses indicate possible errors.'
print >> sys.stderr, ' solve_result_num =', ampl_sol['solve_result_num']
print >> sys.stderr, ' solve_result =', ampl_sol['solve_result']
print >> sys.stderr, ' solve_exitcode =', ampl_sol['solve_exitcode']
print >> sys.stderr, ' '
min_conc_actual = None
max_conc_actual = None
try:
import json
f = open(concentrations_file,'r')
concentrations = json.load(f)
f.close()
qs_idx = concentrations['quality start']
min_conc_actual = min(min(_c for _c in c[qs_idx:] if _c >= concentrations['min quality']) for c in concentrations['nodes'].values())
max_conc_actual = max(max(c[qs_idx:]) for c in concentrations['nodes'].values())
import pylab
from matplotlib.backends.backend_pdf import PdfPages
pylab.figure()
avg = concentrations['min quality']*0.5 + concentrations['max quality']*0.5
pp = PdfPages(os.path.join(os.path.abspath(os.curdir),self.getConfigureOption('output prefix')+'-concentrations-b'+str(max_stations)+'.pdf'))
for node in concentrations['nodes']:
pylab.clf()
pylab.title('Node - '+id_to_name_nodemap[int(node)])
pylab.plot(concentrations['nodes'][node])
pylab.xlabel('Timestep')
pylab.ylabel('Concentration g/m3')
pylab.ylim([max(0,concentrations['min quality']-avg*0.1),concentrations['max quality']+avg*0.1])
pylab.axhline(concentrations['min quality'],color='k',linestyle='--')
pylab.axhline(concentrations['max quality'],color='k',linestyle='--')
pylab.axvline(concentrations['quality start'],color='k')
pylab.savefig(pp,format='pdf')
pp.close()
f = open(mass_injections_file,'r')
mass_injections = json.load(f)
f.close()
pylab.figure()
pp = PdfPages(os.path.join(os.path.abspath(os.curdir),self.getConfigureOption('output prefix')+'-mass-injections-b'+str(max_stations)+'.pdf'))
for node in mass_injections['nodes']:
if max(mass_injections['nodes'][node]) > 0.0:
pylab.clf()
pylab.title('Node - '+id_to_name_nodemap[int(node)])
pylab.plot(mass_injections['nodes'][node])
pylab.xlabel('Timestep')
pylab.ylabel('Mass Injected (Scaled by flow) g/m3')
pylab.ylim([0,1.1*max(mass_injections['nodes'][node][k] for k in range(mass_injections['quality start'],len(mass_injections['nodes'][node])))])
pylab.axvline(concentrations['quality start'],color='k')
pylab.savefig(pp,format='pdf')
pp.close()
except:
print >> sys.stderr, ' '
print >> sys.stderr, 'Failed to generate plot pdf'
print >> sys.stderr, ' '
raise
Solution['objective'] = ampl_sol['objective']
Solution['injected mass grams'] = ampl_sol['injected mass grams']
Solution['average setpoint deviation'] = ampl_sol['average setpoint deviation']
Solution['quality period minutes'] = ampl_sol['quality period minutes']
Solution['min quality bound'] = ampl_sol['min quality']
Solution['min quality actual'] = min_conc_actual
Solution['max quality bound'] = ampl_sol['max quality']
Solution['max quality actual'] = max_conc_actual
Solution['booster nodes'] = [id_to_name_nodemap[name] for name in ampl_sol['booster ids']]
Solution['booster nodes'].sort()
else:
raise RuntimeError("Bad model format option")
# Summarize yaml options
Solution['yaml options'] = copy.deepcopy(self.opts)
Solution['yaml options']['booster']['max boosters'] = max_stations
self.printSolutionSummary(Solution)
out_prefix = ""
if self.getConfigureOption('output prefix') not in self.none_list:
out_prefix += self.getConfigureOption('output prefix')+'-'
results_fname = os.path.join(os.path.abspath(os.curdir),out_prefix+"booster_quality-results-b"+str(max_stations)+'.json')
f = open(results_fname,'w')
json.dump(Solution,f,indent=2)
f.close()
return results_fname
self.delta = self.resynth - self.img.data
self.offset, log = measure_offset(self.resynth,
self.img.data,
withLog=1)
print(os.linesep.join(log))
print(self.offset)
if __name__ == "__main__":
cc = CheckCalib(sys.argv[1], sys.argv[2])
cc.integrate()
cc.rebuild()
pylab.ion()
pylab.imshow(cc.delta, aspect="auto", interpolation=None, origin="bottom")
# pylab.show()
six.moves.input("Delta image")
pylab.imshow(cc.img.data,
aspect="auto",
interpolation=None,
origin="bottom")
six.moves.input("raw image")
pylab.imshow(cc.resynth,
aspect="auto",
interpolation=None,
origin="bottom")
six.moves.input("rebuild image")
pylab.clf()
pylab.plot(cc.r, cc.I)
six.moves.input("powder pattern")
from pylab import plot, xlabel, ylabel, savefig, clf, sin
from numpy import arange
from os import system
t = arange(-6.3, 6.3, 0.1)
for i in range(1, 7):
print "i = ", i
clf()
plot(t, sin(i*t))
xlabel('$x$')
ylabel('$\sin(%dx)$' % i)
savefig("sin%d.pdf" % i)
latex = r"""
\documentclass{article}
\usepackage{graphicx}
\usepackage{subfigure}
\begin{document}
\begin{figure}
"""
for i in range(1, 7):
latex += r"""\subfigure[$i=%d$]{
\includegraphics[scale=0.3]{sin%d}"""% (i, i) + "}\n"
latex += r"""
\end{figure}
\end{document}"""
# import some data to play with # The IRIS dataset from scikits.learn import datasets, svm iris = datasets.load_iris() # Some noisy data not correlated E = np.random.normal(size=(len(iris.data), 35)) # Add the noisy data to the informative features x = np.hstack((iris.data, E)) y = iris.target ################################################################################ pl.figure(1) pl.clf() x_indices = np.arange(x.shape[-1]) ################################################################################ # Univariate feature selection from scikits.learn.feature_selection import SelectFpr, f_classif # As a scoring function, we use a F test for classification # We use the default selection function: the 10% most significant # features selector = SelectFpr(f_classif, alpha=0.1) selector.fit(x, y) scores = -np.log10(selector._pvalues) scores /= scores.max() pl.bar(x_indices - .45,
def image(sim,
qty='rho',
width="10 kpc",
resolution=500,
units=None,
log=True,
vmin=None,
vmax=None,
av_z=False,
filename=None,
z_camera=None,
clear=True,
cmap=None,
title=None,
qtytitle=None,
show_cbar=True,
subplot=False,
noplot=False,
ret_im=False,
fill_nan=True,
fill_val=0.0,
linthresh=None,
**kwargs):
"""
Make an SPH image of the given simulation.
**Keyword arguments:**
*qty* (rho): The name of the array to interpolate
*width* (10 kpc): The overall width and height of the plot. If
``width`` is a float or an int, then it is assumed to be in units
of ``sim['pos']``. It can also be passed in as a string
indicating the units, i.e. '10 kpc', in which case it is
converted to units of ``sim['pos']``.
*resolution* (500): The number of pixels wide and tall
*units* (None): The units of the output
*av_z* (False): If True, the requested quantity is averaged down
the line of sight (default False: image is generated in
the thin plane z=0, unless output units imply an integral
down the line of sight). If a string, the requested quantity
is averaged down the line of sight weighted by the av_z
array (e.g. use 'rho' for density-weighted quantity;
the default results when av_z=True are volume-weighted).
*z_camera* (None): If set, a perspective image is rendered. See
:func:`pynbody.sph.image` for more details.
*filename* (None): if set, the image will be saved in a file
*clear* (True): whether to call clf() on the axes first
*cmap* (None): user-supplied colormap instance
*title* (None): plot title
*qtytitle* (None): colorbar quantity title
*show_cbar* (True): whether to plot the colorbar
*subplot* (False): the user can supply a AxesSubPlot instance on
which the image will be shown
*noplot* (False): do not display the image, just return the image array
*ret_im* (False): return the image instance returned by imshow
*num_threads* (None) : if set, specify the number of threads for
the multi-threaded routines; otherwise the pynbody.config default is used
*fill_nan* (True): if any of the image values are NaN, replace with fill_val
*fill_val* (0.0): the fill value to use when replacing NaNs
*linthresh* (None): if the image has negative and positive values
and a log scaling is requested, the part between `-linthresh` and
`linthresh` is shown on a linear scale to avoid divergence at 0
"""
if not noplot:
import matplotlib.pylab as plt
global config
if not noplot:
if subplot:
p = subplot
else:
p = plt
if qtytitle is None:
qtytitle = qty
if isinstance(units, str):
units = _units.Unit(units)
if isinstance(width, str) or issubclass(width.__class__, _units.UnitBase):
if isinstance(width, str):
width = _units.Unit(width)
width = width.in_units(sim['pos'].units, **sim.conversion_context())
width = float(width)
kernel = sph.Kernel()
perspective = z_camera is not None
if perspective and not av_z:
kernel = sph.Kernel2D()
is_projected = False
if units is not None:
is_projected = _units_imply_projection(sim, qty, units)
if is_projected:
kernel = sph.Kernel2D()
if av_z:
if isinstance(kernel, sph.Kernel2D):
raise _units.UnitsException(
"Units already imply projected image; can't also average over line-of-sight!"
)
else:
kernel = sph.Kernel2D()
if units is not None:
aunits = units * sim['z'].units
else:
aunits = None
if isinstance(av_z, str):
if units is not None:
aunits = units * sim[av_z].units * sim['z'].units
sim["__prod"] = sim[av_z] * sim[qty]
qty = "__prod"
else:
av_z = "__one"
sim["__one"] = np.ones_like(sim[qty])
sim["__one"].units = "1"
im = sph.render_image(sim,
qty,
width / 2,
resolution,
out_units=aunits,
kernel=kernel,
z_camera=z_camera,
**kwargs)
im2 = sph.render_image(sim,
av_z,
width / 2,
resolution,
kernel=kernel,
z_camera=z_camera,
**kwargs)
top = sim.ancestor
try:
del top["__one"]
except KeyError:
pass
try:
del top["__prod"]
except KeyError:
pass
im = im / im2
else:
im = sph.render_image(sim,
qty,
width / 2,
resolution,
out_units=units,
kernel=kernel,
z_camera=z_camera,
**kwargs)
if fill_nan:
im[np.isnan(im)] = fill_val
if not noplot:
# set the log or linear normalizations
if log:
try:
im[np.where(im == 0)] = abs(im[np.where(abs(im != 0))]).min()
except ValueError:
raise ValueError(
"Failed to make a sensible logarithmic image. This probably means there are no particles in the view."
)
# check if there are negative values -- if so, use the symmetric
# log normalization
if (vmin is None and
(im < 0).any()) or ((vmin is not None) and vmin < 0):
# need to set the linear regime around zero -- set to by
# default start at 1/1000 of the log range
if linthresh is None:
linthresh = np.nanmax(abs(im)) / 1000.
norm = matplotlib.colors.SymLogNorm(linthresh,
vmin=vmin,
vmax=vmax)
else:
norm = matplotlib.colors.LogNorm(vmin=vmin, vmax=vmax)
else:
norm = matplotlib.colors.Normalize(vmin=vmin, vmax=vmax)
#
# do the actual plotting
#
if clear and not subplot:
p.clf()
if ret_im:
return p.imshow(im[::-1, :].view(np.ndarray),
extent=(-width / 2, width / 2, -width / 2,
width / 2),
vmin=vmin,
vmax=vmax,
cmap=cmap,
norm=norm)
ims = p.imshow(im[::-1, :].view(np.ndarray),
extent=(-width / 2, width / 2, -width / 2, width / 2),
vmin=vmin,
vmax=vmax,
cmap=cmap,
norm=norm)
u_st = sim['pos'].units.latex()
if not subplot:
plt.xlabel("$x/%s$" % u_st)
plt.ylabel("$y/%s$" % u_st)
else:
p.set_xlabel("$x/%s$" % u_st)
p.set_ylabel("$y/%s$" % u_st)
if units is None:
units = im.units
if units.latex() == "":
units = ""
else:
units = "$" + units.latex() + "$"
if show_cbar:
plt.colorbar(ims).set_label(qtytitle + "/" + units)
# colorbar doesn't work wtih subplot: mappable is NoneType
# elif show_cbar:
# import matplotlib.pyplot as mpl
# if qtytitle: mpl.colorbar().set_label(qtytitle)
# else: mpl.colorbar().set_label(units)
if title is not None:
if not subplot:
p.title(title)
else:
p.set_title(title)
if filename is not None:
p.savefig(filename)
plt.draw()
# plt.show() - removed by AP on 30/01/2013 - this should not be here as
# for some systems you don't get back to the command prompt
return im
def mctweak(wcs, xy, rd):
obj = McTweak(wcs, xy, rd)
# Initial args
args, sigs = get_sip_args(wcs)
print('Args:', args)
print('Sigs:', sigs)
print('Number of arguments:', len(args))
print('Logodds:', obj(args))
ndim, nwalkers = len(args), 100
p0 = emcee.utils.sample_ball(args, sigs, size=nwalkers)
print('p0', p0.shape)
ps = PlotSequence('mctweak')
W, H = wcs.get_width(), wcs.get_height()
mywcs = Sip(wcs)
sampler = emcee.EnsembleSampler(nwalkers, ndim, obj)
lnp0, rstate = None, None
pp = []
for step in range(10000):
print('Step', step)
p0, lnp0, rstate = sampler.run_mcmc(p0,
1,
lnprob0=lnp0,
rstate0=rstate)
print('Best logprob:', np.max(lnp0))
i = np.argmax(lnp0)
print('Best args:', p0[i, :])
pp.extend(sampler.flatchain)
sampler.reset()
if step % 100 != 0:
continue
plt.clf()
plt.plot(obj.testxy[:, 0], obj.testxy[:, 1], 'r.')
for args in p0[np.random.permutation(nwalkers)[:10], :]:
set_sip_args(mywcs, args)
sip_compute_inverse_polynomials(mywcs, 20, 20, 1, W, 1, H)
ok, x, y = mywcs.radec2pixelxy(obj.refra, obj.refdec)
plt.plot(x, y, 'bo', mec='b', mfc='none', alpha=0.25)
ex = 10.
ngridx = ngridy = 10
stepx = stepy = 100
xgrid = np.linspace(0, W, ngridx)
ygrid = np.linspace(0, H, ngridy)
X = np.linspace(0, W, int(np.ceil(W / stepx)))
Y = np.linspace(0, H, int(np.ceil(H / stepy)))
for x in xgrid:
DX, DY = [], []
xx, yy = [], []
for y in Y:
dx, dy = mywcs.get_distortion(x, y)
xx.append(x)
yy.append(y)
DX.append(dx)
DY.append(dy)
DX = np.array(DX)
DY = np.array(DY)
xx = np.array(xx)
yy = np.array(yy)
EX = DX + ex * (DX - xx)
EY = DY + ex * (DY - yy)
#plot(xx, yy, 'k-', alpha=0.5)
plt.plot(EX, EY, 'b-', alpha=0.1)
for y in ygrid:
DX, DY = [], []
xx, yy = [], []
for x in X:
dx, dy = mywcs.get_distortion(x, y)
DX.append(dx)
DY.append(dy)
xx.append(x)
yy.append(y)
DX = np.array(DX)
DY = np.array(DY)
xx = np.array(xx)
yy = np.array(yy)
EX = DX + ex * (DX - xx)
EY = DY + ex * (DY - yy)
#plot(xx, yy, 'k-', alpha=0.5)
plt.plot(EX, EY, 'b-', alpha=0.1)
for x in xgrid:
plt.plot(x + np.zeros_like(Y), Y, 'k-', alpha=0.5)
for y in ygrid:
plt.plot(X, y + np.zeros_like(X), 'k-', alpha=0.5)
plt.axis([1, W, 1, H])
plt.axis('scaled')
ps.savefig()
pp = np.vstack(pp)
print('pp', pp.shape)
# plt.clf()
# triangle.corner(pp, plot_contours=False)
# ps.savefig()
pp = []
def do_all_angles(rootname='sv',
smooth=21,
wmin=850,
wmax=1850,
fmax=0,
fig_no=1,
title=None):
'''
Plot each of the spectra where
smooth is the number of bins to boxcar smooth
fmax sets the ylim of the plot, assuming it is not zero
and other values should be obvious.
140907 ksl Updated to include fmax
140912 ksl Updated so uses rootname
141124 ksl Updated for new formats which use astropy
'''
filename = rootname + '.spec'
try:
data = ascii.read(filename)
except IOError:
print('Error: Could not find %s' % filename)
return 'None'
# print(data.colnames)
# Now determine what the coluns containing real spectra are
# while makeing the manes simpler
cols = []
i = 9
while i < len(data.colnames):
one = data.colnames[i]
# print 'gotcha',one
new_name = one.replace('P0.50', '')
new_name = new_name.replace('A', '')
data.rename_column(one, new_name)
cols.append(new_name)
i = i + 1
root = rootname
# if wmin and wmax are not specified, use wmin and wmax from input file
if wmin == 0 or wmax == 0:
xwave = numpy.array(data['Lambda'])
xmin = numpy.min(xwave)
xmax = numpy.max(xwave)
if wmin == 0:
wmin = xmin
if wmax == 0:
wmax = xmax
pylab.figure(fig_no, (9, 6))
pylab.clf()
# print(cols)
for col in cols:
flux = data[col]
# print(flux)
xlabel = col + '$^{\circ}$'
q = convolve(flux, boxcar(smooth) / float(smooth), mode='same')
pylab.plot(data['Lambda'], q, '-', label=xlabel)
pylab.xlabel(r'Wavelength ($\AA$)', size=16)
pylab.ylabel('Flux', size=16)
z = pylab.axis()
if fmax == 0:
pylab.axis((wmin, wmax, 0, z[3]))
else:
pylab.axis((wmin, wmax, 0, fmax))
if title == None:
title = root
pylab.title(title, size=16)
pylab.legend(loc='best')
pylab.draw()
plotfile = root + '.png'
pylab.savefig(plotfile)
return plotfile
def __print_stars(clist, smax, sig, out=True, save=None, data=None, imgw=None):
#TODO: set the scale correctly for each graph
import pylab
global rejected, texts
nx = int(np.sqrt(smax))
ny = nx + 2
i = 1
im1 = []
im2 = []
im3 = []
im4 = []
im5 = []
rejected = []
texts = []
slist = []
pylab.figure(1)
for c in clist:
if c.grade > 2:
print c
slist += [c]
pylab.subplot(nx, ny, i)
pylab.title('candidate ' + str(i))
extent = (0, c.img.shape[1], 0, c.img.shape[0])
im1 += [
pylab.imshow(c.img, extent=extent, interpolation="nearest")
]
im2 += [
pylab.imshow(c.chi,
extent=extent,
hold=True,
interpolation="nearest")
]
pylab.colorbar(im2[-1])
im2[-1].set_visible(False)
if sig is not None:
chisig1 = c.chi.copy()
chisig2 = c.chi.copy()
chisig3 = c.chi.copy()
chisig1[np.where(abs(chisig1) > sig)] = 0.
chisig2[np.where(abs(chisig2) > 2. * sig)] = 0.
chisig3[np.where(abs(chisig3) > 3. * sig)] = 0.
im3 += [
pylab.imshow(chisig1,
extent=extent,
hold=True,
interpolation="nearest")
]
im4 += [
pylab.imshow(chisig2,
extent=extent,
hold=True,
interpolation="nearest")
]
im5 += [
pylab.imshow(chisig3,
extent=extent,
hold=True,
interpolation="nearest")
]
im3[-1].set_visible(False)
im4[-1].set_visible(False)
im5[-1].set_visible(False)
i += 1
def toggle_images(event):
key = event.key
keys = '0'
if sig is not None:
keys = '1230'
b1 = im1[0].get_visible()
b2 = im2[0].get_visible() or b1 == False
if key not in keys:
return
for im in im1:
im.set_visible(not b1 and key == '0')
for im in im2:
im.set_visible(not b2 and key == '0')
if sig is not None:
for im in im3:
im.set_visible(key == '1')
for im in im4:
im.set_visible(key == '2')
for im in im5:
im.set_visible(key == '3')
pylab.draw()
def click(event):
canvas = event.canvas
if event.inaxes and event.xdata > 1. and event.ydata > 1.:
global rejected, texts
for i, ax in enumerate(rejected):
if event.inaxes is ax:
event.inaxes.texts.remove(texts[i])
del rejected[i]
del texts[i]
break
else:
texts += [
event.inaxes.annotate('REMOVED', xy=(1, 1), color='red')
]
rejected += [event.inaxes]
pylab.draw()
pylab.connect('key_press_event', toggle_images)
pylab.connect('button_press_event', click)
if save != None:
import src.lib.AImage, ImageDraw, Image
#from PIL import Image
split = save.split('.')
ext = '.' + split[-1]
del split[-1]
base = ''
for s in split:
base += s + '.'
if base[-1] == '.': base = base[:-1]
split = save.split('/')[0:-1]
dir = ''
for s in split:
dir += s + '/'
pylab.savefig(save)
for im in im2:
im.set_visible(True)
for im in im1:
im.set_visible(False)
pylab.savefig(base + '_sig' + ext)
for im in im3:
im.set_visible(True)
for im in im2:
im.set_visible(False)
pylab.savefig(base + '_1sig' + ext)
for im in im4:
im.set_visible(True)
for im in im3:
im.set_visible(False)
pylab.savefig(base + '_2sig' + ext)
for im in im5:
im.set_visible(True)
for im in im4:
im.set_visible(False)
pylab.savefig(base + '_3sig' + ext)
img = fn.makepilimage(src.lib.AImage.Image(data))
img = img.convert("RGB")
draw = ImageDraw.Draw(img)
for c in clist:
if c.grade > 2:
draw.text((c.x, c.y - c.rad[0] - 10),
str(c.id),
fill="#00ff00")
draw.ellipse([(c.x - c.rad[0], c.y - c.rad[1]),
(c.x + c.rad[1], c.y + c.rad[0])],
outline="#00ff00")
else:
draw.ellipse([(c.x - c.rad[0], c.y - c.rad[1]),
(c.x + c.rad[1], c.y + c.rad[0])],
outline=(255, 0, 0)) #"#ff0000")
draw.text((c.x, c.y - c.rad[0] - 10),
str(c.id),
fill="#ff0000")
r = max(c.rad) + 10
thumb = img.crop((c.x - r, c.y - r, c.x + r, c.y + r))
thumb = thumb.resize((128, 128), Image.ANTIALIAS)
thumb.save(dir + 'thumb/candidate_' + str(c.id) + '.png', "PNG")
del draw
if imgw is not None:
low = img.resize((imgw, img.size[1] * imgw / img.size[0]),
Image.ANTIALIAS)
low.save(base + '_img_low.png', "PNG")
img.save(base + '_img.png', "PNG")
if out == True:
pylab.show()
final_slist = []
for i, im in enumerate(im1):
for ax in rejected:
if ax is im.get_axes():
break
else:
final_slist += [slist[i]]
pylab.clf()
return final_slist
def plot_stress_fields(atoms, r_range=None, initial_params=None, fix_params=None,
sigma=None, avg_sigma=None, avg_decay=0.005, calc=None):
"""
Fit and plot atomistic and continuum stress fields
Firstly a fit to the Irwin `K`-field solution is carried out using
:func:`fit_crack_stress_field`, and parameters have the same
meaning as for that function. Then plots of the
:math:`\sigma_{xx}`, :math:`\sigma_{yy}`, :math:`\sigma_{xy}`
fields are produced for atomistic and continuum cases, and for the
residual error after fitting.
"""
from pylab import griddata, meshgrid, subplot, cla, contourf, colorbar, draw, title, clf, gca
params, err = fit_crack_stress_field(atoms, r_range, initial_params, fix_params, sigma,
avg_sigma, avg_decay, calc)
K, x0, y0, sxx0, syy0, sxy0 = (params['K'], params['x0'], params['y0'],
params['sxx0'], params['syy0'], params['sxy0'])
x = atoms.positions[:, 0]
y = atoms.positions[:, 1]
X = np.linspace((x-x0).min(), (x-x0).max(), 500)
Y = np.linspace((y-y0).min(), (y-y0).max(), 500)
t = np.arctan2(y-y0, x-x0)
r = np.sqrt((x-x0)**2 + (y-y0)**2)
if r_range is not None:
rmin, rmax = r_range
mask = (r > rmin) & (r < rmax)
else:
mask = Ellipsis
atom_sigma = sigma
if atom_sigma is None:
atom_sigma = atoms.get_stresses()
grid_sigma = np.dstack([griddata(x[mask]-x0, y[mask]-y0, atom_sigma[mask,0,0], X, Y),
griddata(x[mask]-x0, y[mask]-y0, atom_sigma[mask,1,1], X, Y),
griddata(x[mask]-x0, y[mask]-y0, atom_sigma[mask,0,1], X, Y)])
X, Y = meshgrid(X, Y)
R = np.sqrt(X**2+Y**2)
T = np.arctan2(Y, X)
grid_sigma[((R < rmin) | (R > rmax)),:] = np.nan # mask outside fitting region
isotropic_sigma = isotropic_modeI_crack_tip_stress_field(K, R, T, x0, y0)
isotropic_sigma[...,0,0] += sxx0
isotropic_sigma[...,1,1] += syy0
isotropic_sigma[...,0,1] += sxy0
isotropic_sigma[...,1,0] += sxy0
isotropic_sigma = ma.masked_array(isotropic_sigma, mask=grid_sigma.mask)
isotropic_sigma[((R < rmin) | (R > rmax)),:,:] = np.nan # mask outside fitting region
contours = [np.linspace(0, 20, 10),
np.linspace(0, 20, 10),
np.linspace(-10,10, 10)]
dcontours = [np.linspace(0, 5, 10),
np.linspace(0, 5, 10),
np.linspace(-5, 5, 10)]
clf()
for i, (ii, jj), label in zip(range(3),
[(0,0), (1,1), (0,1)],
['\sigma_{xx}', r'\sigma_{yy}', r'\sigma_{xy}']):
subplot(3,3,i+1)
gca().set_aspect('equal')
contourf(X, Y, grid_sigma[...,i]*GPA, contours[i])
colorbar()
title(r'$%s^\mathrm{atom}$' % label)
draw()
subplot(3,3,i+4)
gca().set_aspect('equal')
contourf(X, Y, isotropic_sigma[...,ii,jj]*GPA, contours[i])
colorbar()
title(r'$%s^\mathrm{Isotropic}$' % label)
draw()
subplot(3,3,i+7)
gca().set_aspect('equal')
contourf(X, Y, abs(grid_sigma[...,i] -
isotropic_sigma[...,ii,jj])*GPA, dcontours[i])
colorbar()
title(r'$|%s^\mathrm{atom} - %s^\mathrm{isotropic}|$' % (label, label))
draw()
def wise_cutouts(ra,
dec,
radius,
ps,
pixscale=2.75,
tractor_base='.',
unwise_dir='unwise-coadds'):
'''
radius in arcsec.
pixscale: WISE pixel scale in arcsec/pixel;
make this smaller than 2.75 to oversample.
'''
npix = int(np.ceil(radius / pixscale))
print('Image size:', npix)
W = H = npix
pix = pixscale / 3600.
wcs = Tan(ra, dec, (W + 1) / 2., (H + 1) / 2., -pix, 0., 0., pix, float(W),
float(H))
# Find DECaLS bricks overlapping
decals = Decals()
B = bricks_touching_wcs(wcs, decals=decals)
print('Found', len(B), 'bricks overlapping')
TT = []
for b in B.brickname:
fn = os.path.join(tractor_base, 'tractor', b[:3],
'tractor-%s.fits' % b)
T = fits_table(fn)
print('Read', len(T), 'from', b)
primhdr = fitsio.read_header(fn)
TT.append(T)
T = merge_tables(TT)
print('Total of', len(T), 'sources')
T.cut(T.brick_primary)
print(len(T), 'primary')
margin = 20
ok, xx, yy = wcs.radec2pixelxy(T.ra, T.dec)
I = np.flatnonzero((xx > -margin) * (yy > -margin) * (xx < W + margin) *
(yy < H + margin))
T.cut(I)
print(len(T), 'within ROI')
# Pull out DECaLS coadds (image, model, resid).
dwcs = wcs.scale(2. * pixscale / 0.262)
dh, dw = dwcs.shape
print('DECaLS resampled shape:', dh, dw)
tags = ['image', 'model', 'resid']
coimgs = [np.zeros((dh, dw, 3), np.uint8) for t in tags]
for b in B.brickname:
fn = os.path.join(tractor_base, 'coadd', b[:3], b,
'decals-%s-image-r.fits' % b)
bwcs = Tan(fn)
try:
Yo, Xo, Yi, Xi, nil = resample_with_wcs(dwcs, bwcs)
except ResampleError:
continue
if len(Yo) == 0:
continue
print('Resampling', len(Yo), 'pixels from', b)
xl, xh, yl, yh = Xi.min(), Xi.max(), Yi.min(), Yi.max()
print(
'python legacypipe/runbrick.py -b %s --zoom %i %i %i %i --outdir cluster --pixpsf --splinesky --pipe --no-early-coadds'
% (b, xl - 5, xh + 5, yl - 5, yh + 5) +
' -P \'pickles/cluster-%(brick)s-%%(stage)s.pickle\'')
for i, tag in enumerate(tags):
fn = os.path.join(tractor_base, 'coadd', b[:3], b,
'decals-%s-%s.jpg' % (b, tag))
img = plt.imread(fn)
img = np.flipud(img)
coimgs[i][Yo, Xo, :] = img[Yi, Xi, :]
tt = dict(image='Image', model='Model', resid='Resid')
for img, tag in zip(coimgs, tags):
plt.clf()
dimshow(img, ticks=False)
plt.title('DECaLS grz %s' % tt[tag])
ps.savefig()
# Find unWISE tiles overlapping
tiles = unwise_tiles_touching_wcs(wcs)
print('Cut to', len(tiles), 'unWISE tiles')
# Here we assume the targetwcs is axis-aligned and that the
# edge midpoints yield the RA,Dec limits (true for TAN).
r, d = wcs.pixelxy2radec(np.array([1, W, W / 2, W / 2]),
np.array([H / 2, H / 2, 1, H]))
# the way the roiradec box is used, the min/max order doesn't matter
roiradec = [r[0], r[1], d[2], d[3]]
ra, dec = T.ra, T.dec
T.shapeexp = np.vstack((T.shapeexp_r, T.shapeexp_e1, T.shapeexp_e2)).T
T.shapedev = np.vstack((T.shapedev_r, T.shapedev_e1, T.shapedev_e2)).T
srcs = read_fits_catalog(T, ellipseClass=EllipseE)
wbands = [1, 2]
wanyband = 'w'
for band in wbands:
T.wise_flux[:, band - 1] *= 10.**(primhdr['WISEAB%i' % band] / 2.5)
coimgs = [np.zeros((H, W), np.float32) for b in wbands]
comods = [np.zeros((H, W), np.float32) for b in wbands]
con = [np.zeros((H, W), np.uint8) for b in wbands]
for iband, band in enumerate(wbands):
print('Photometering WISE band', band)
wband = 'w%i' % band
for i, src in enumerate(srcs):
#print('Source', src, 'brightness', src.getBrightness(), 'params', src.getBrightness().getParams())
#src.getBrightness().setParams([T.wise_flux[i, band-1]])
src.setBrightness(
NanoMaggies(**{wanyband: T.wise_flux[i, band - 1]}))
# print('Set source brightness:', src.getBrightness())
# The tiles have some overlap, so for each source, keep the
# fit in the tile whose center is closest to the source.
for tile in tiles:
print('Reading tile', tile.coadd_id)
tim = get_unwise_tractor_image(unwise_dir,
tile.coadd_id,
band,
bandname=wanyband,
roiradecbox=roiradec)
if tim is None:
print('Actually, no overlap with tile', tile.coadd_id)
continue
print('Read image with shape', tim.shape)
# Select sources in play.
wisewcs = tim.wcs.wcs
H, W = tim.shape
ok, x, y = wisewcs.radec2pixelxy(ra, dec)
x = (x - 1.).astype(np.float32)
y = (y - 1.).astype(np.float32)
margin = 10.
I = np.flatnonzero((x >= -margin) * (x < W + margin) *
(y >= -margin) * (y < H + margin))
print(len(I), 'within the image + margin')
subcat = [srcs[i] for i in I]
tractor = Tractor([tim], subcat)
mod = tractor.getModelImage(0)
# plt.clf()
# dimshow(tim.getImage(), ticks=False)
# plt.title('WISE %s %s' % (tile.coadd_id, wband))
# ps.savefig()
# plt.clf()
# dimshow(mod, ticks=False)
# plt.title('WISE %s %s' % (tile.coadd_id, wband))
# ps.savefig()
try:
Yo, Xo, Yi, Xi, nil = resample_with_wcs(wcs, tim.wcs.wcs)
except ResampleError:
continue
if len(Yo) == 0:
continue
print('Resampling', len(Yo), 'pixels from WISE', tile.coadd_id,
band)
coimgs[iband][Yo, Xo] += tim.getImage()[Yi, Xi]
comods[iband][Yo, Xo] += mod[Yi, Xi]
con[iband][Yo, Xo] += 1
for img, mod, n in zip(coimgs, comods, con):
img /= np.maximum(n, 1)
mod /= np.maximum(n, 1)
for band, img, mod in zip(wbands, coimgs, comods):
lo, hi = np.percentile(img, [25, 99])
plt.clf()
dimshow(img, vmin=lo, vmax=hi, ticks=False)
plt.title('WISE W%i Data' % band)
ps.savefig()
plt.clf()
dimshow(mod, vmin=lo, vmax=hi, ticks=False)
plt.title('WISE W%i Model' % band)
ps.savefig()
resid = img - mod
mx = np.abs(resid).max()
plt.clf()
dimshow(resid, vmin=-mx, vmax=mx, ticks=False)
plt.title('WISE W%i Resid' % band)
ps.savefig()
#kwa = dict(mn=-0.1, mx=2., arcsinh = 1.)
kwa = dict(mn=-0.1, mx=2., arcsinh=None)
rgb = _unwise_to_rgb(coimgs, **kwa)
plt.clf()
dimshow(rgb, ticks=False)
plt.title('WISE W1/W2 Data')
ps.savefig()
rgb = _unwise_to_rgb(comods, **kwa)
plt.clf()
dimshow(rgb, ticks=False)
plt.title('WISE W1/W2 Model')
ps.savefig()
kwa = dict(mn=-1, mx=1, arcsinh=None)
rgb = _unwise_to_rgb([img - mod for img, mod in zip(coimgs, comods)],
**kwa)
plt.clf()
dimshow(rgb, ticks=False)
plt.title('WISE W1/W2 Resid')
ps.savefig()
def run(self):
"""
2007-03-29
2007-04-03
2007-05-01
--db_connect()
--FilterStrainSNPMatrix_instance.read_data()
if self.comparison_only:
--FilterStrainSNPMatrix_instance.read_data()
else:
--get_SNPpos2index()
--create_SNP_matrix_2010()
--get_align_length_from_fname()
--get_positions_to_be_checked_ls()
--get_align_matrix_from_fname()
--get_positions_to_be_checked_ls()
--get_mapping_info_regarding_strain_acc()
--shuffle_data_matrix_according_to_strain_acc_ls()
--FilterStrainSNPMatrix_instance.write_data_matrix()
--extract_sub_data_matrix()
if self.sub_justin_output_fname:
--FilterStrainSNPMatrix_instance.write_data_matrix()
--compare_two_SNP_matrix()
--outputDiffType()
"""
from FilterStrainSNPMatrix import FilterStrainSNPMatrix
FilterStrainSNPMatrix_instance = FilterStrainSNPMatrix()
header, src_strain_acc_list, category_list, data_matrix = FilterStrainSNPMatrix_instance.read_data(
self.input_fname)
if self.comparison_only:
header, strain_acc_ls, abbr_name_ls_sorted, SNP_matrix_2010_sorted = FilterStrainSNPMatrix_instance.read_data(
self.output_fname)
SNP_matrix_2010_sorted = Numeric.array(SNP_matrix_2010_sorted)
else:
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
#extract data from alignment
snp_acc_ls = header[2:]
SNPpos2index = self.get_SNPpos2index(curs, snp_acc_ls,
self.snp_locus_table)
abbr_name_ls, SNP_matrix_2010 = self.create_SNP_matrix_2010(
SNPpos2index, self.data_dir_2010)
strain_acc_ls, strain_acc2abbr_name, strain_acc2index = self.get_mapping_info_regarding_strain_acc(
curs, self.strain_info_table, self.strain_info_2010_table,
abbr_name_ls)
SNP_matrix_2010_sorted = self.shuffle_data_matrix_according_to_strain_acc_ls(
SNP_matrix_2010, strain_acc_ls, strain_acc2index)
abbr_name_ls_sorted = []
for strain_acc in strain_acc_ls:
abbr_name_ls_sorted.append(strain_acc2abbr_name[strain_acc])
FilterStrainSNPMatrix_instance.write_data_matrix(
SNP_matrix_2010_sorted, self.output_fname, header,
strain_acc_ls, abbr_name_ls_sorted)
#comparison
data_matrix = Numeric.array(data_matrix)
sub_data_matrix = self.extract_sub_data_matrix(src_strain_acc_list,
data_matrix,
strain_acc_ls)
if self.sub_justin_output_fname:
FilterStrainSNPMatrix_instance.write_data_matrix(
sub_data_matrix, self.sub_justin_output_fname, header,
strain_acc_ls, abbr_name_ls_sorted)
diff_matrix, diff_tag_dict, diff_tag2counter = self.compare_two_SNP_matrix(
SNP_matrix_2010_sorted, sub_data_matrix)
if self.diff_output_fname:
self.outputDiffType(diff_matrix, SNP_matrix_2010_sorted,
sub_data_matrix, diff_tag_dict,
self.diff_type_to_be_outputted,
abbr_name_ls_sorted, header[2:],
self.diff_output_fname)
summary_result_ls = []
for tag, counter in diff_tag2counter.iteritems():
summary_result_ls.append('%s(%s):%s' %
(tag, diff_tag_dict[tag], counter))
print '\t%s(%s)\t%s' % (tag, diff_tag_dict[tag], counter)
import pylab
pylab.clf()
diff_matrix_reverse = list(diff_matrix)
diff_matrix_reverse.reverse()
diff_matrix_reverse = Numeric.array(diff_matrix_reverse)
pylab.imshow(diff_matrix_reverse, interpolation='nearest')
pylab.title(' '.join(summary_result_ls))
pylab.colorbar()
pylab.show()
#2007-11-01 do something as CmpAccession2Ecotype.py
from CmpAccession2Ecotype import CmpAccession2Ecotype
CmpAccession2Ecotype_ins = CmpAccession2Ecotype()
nt_number2diff_matrix_index = CmpAccession2Ecotype_ins.get_nt_number2diff_matrix_index(
nt2number)
dc_placeholder = dict(
zip(range(sub_data_matrix.shape[0]),
range(sub_data_matrix.shape[1])))
diff_matrix_ls = CmpAccession2Ecotype_ins.cmp_two_matricies(
SNP_matrix_2010_sorted, sub_data_matrix,
nt_number2diff_matrix_index, dc_placeholder, dc_placeholder,
dc_placeholder)
print diff_matrix_ls
def do_all_angles_ev(rootname='sv',
smooth=21,
emin=1000,
emax=9000,
fmax=0,
fig_no=1):
'''
Plot each of the spectra where
smooth is the number of bins to boxcar smooth
fmax sets the ylim of the plot, assuming it is not zero
and other values should be obvious.
160405 ksl This version of the routine is intended to plot the X-ray
regime
'''
if rootname.count('.') > 0:
filename = rootname
rootname = rootname[0:rootname.rindex('.')]
# print('test',rootname)
else:
filename = rootname + '.spec'
try:
data = ascii.read(filename)
except IOError:
print('Error: Could not find %s' % filename)
return 'None'
print(data.colnames)
HEV = 4.136e-15
# Now determine what the coluns containing real spectra are
# while makeing the manes simpler
cols = []
i = 9
while i < len(data.colnames):
one = data.colnames[i]
# print 'gotcha',one
new_name = one.replace('P0.50', '')
new_name = new_name.replace('A', '')
data.rename_column(one, new_name)
cols.append(new_name)
i = i + 1
root = rootname
pylab.figure(fig_no, (9, 6))
pylab.clf()
for col in cols:
flux = data[col]
# print(flux)
xlabel = col + '$^{\circ}$'
q = convolve(flux, boxcar(smooth) / float(smooth), mode='same')
pylab.semilogx(data['Freq.'] * HEV,
q * data['Freq.'],
'-',
label=xlabel)
pylab.xlabel(r'Energy (eV)', size=16)
pylab.ylabel(r'$\nu F_{\nu}$', size=16)
z = pylab.axis()
if fmax == 0:
pylab.axis((emin, emax, 0, z[3]))
else:
pylab.axis((emin, emax, 0, fmax))
pylab.title(root)
pylab.legend(loc='best')
pylab.draw()
plotfile = root + '.png'
pylab.savefig(plotfile)
return plotfile
def search(tile):
if os.path.exists('rogue-%s-02.png' %
tile) and not os.path.exists('rogue-%s-03.png' % tile):
print 'Skipping', tile
return
fn = os.path.join(tile[:3], tile, 'unwise-%s-w2-%%s-m.fits' % tile)
try:
II = [fitsio.read(os.path.join('e%i' % e, fn % 'img')) for e in [1, 2]]
PP = [fitsio.read(os.path.join('e%i' % e, fn % 'std')) for e in [1, 2]]
wcs = Tan(os.path.join('e%i' % 1, fn % 'img'))
except:
import traceback
print
print 'Failed to read data for tile', tile
traceback.print_exc()
print
return
H, W = II[0].shape
ps = PlotSequence('rogue-%s' % tile)
aa = dict(interpolation='nearest', origin='lower')
ima = dict(interpolation='nearest', origin='lower', vmin=-100, vmax=500)
plt.clf()
plt.imshow(II[0], **ima)
plt.title('Epoch 1')
ps.savefig()
plt.clf()
plt.imshow(II[1], **ima)
plt.title('Epoch 2')
ps.savefig()
# X = gaussian_filter(np.abs((II[0] - II[1]) / np.hypot(PP[0], PP[1])), 1.0)
# plt.clf()
# plt.imshow(X, interpolation='nearest', origin='lower')
# plt.title('Blurred abs difference / per-pixel-std')
# ps.savefig()
# Y = (II[0] - II[1]) / reduce(np.hypot, [PP[0], PP[1], np.hypot(100,II[0]), np.hypot(100,II[1]) ])
Y = (II[0] - II[1]) / reduce(np.hypot, [PP[0], PP[1]])
X = gaussian_filter(np.abs(Y), 1.0)
xthresh = 3.
print 'Value at rogue:', X[1452, 1596]
print 'pp at rogue:', [pp[1452, 1596] for pp in PP]
plt.clf()
plt.imshow(X, interpolation='nearest', origin='lower')
plt.title('X')
ps.savefig()
# plt.clf()
# plt.hist(np.minimum(100, PP[0].ravel()), 100, range=(0,100),
# histtype='step', color='r')
# plt.hist(np.minimum(100, PP[1].ravel()), 100, range=(0,100),
# histtype='step', color='b')
# plt.title('Per-pixel std')
# ps.savefig()
#Y = ((II[0] - II[1]) / np.hypot(PP[0], PP[1]))
#Y = gaussian_filter(
# (II[0] - II[1]) / np.hypot(100, np.hypot(II[0], II[1]))
# , 1.0)
#I = np.argsort(-X.ravel())
#yy,xx = np.unravel_index(I[:25], X.shape)
#print 'xx', xx
#print 'yy', yy
hot = (X > xthresh)
peak = find_peaks(hot, X)
dilate = 2
hot = binary_dilation(hot, structure=np.ones((3, 3)), iterations=dilate)
blobs, nblobs = label(hot, np.ones((3, 3), int))
blobslices = find_objects(blobs)
# Find maximum pixel within each blob.
BX, BY = [], []
BV = []
for b, slc in enumerate(blobslices):
sy, sx = slc
y0, y1 = sy.start, sy.stop
x0, x1 = sx.start, sx.stop
bl = blobs[slc]
i = np.argmax((bl == (b + 1)) * X[slc])
iy, ix = np.unravel_index(i, dims=bl.shape)
by = iy + y0
bx = ix + x0
BX.append(bx)
BY.append(by)
BV.append(X[by, bx])
BX = np.array(BX)
BY = np.array(BY)
BV = np.array(BV)
I = np.argsort(-BV)
xx, yy = BX[I], BY[I]
keep = []
S = 15
for i, (x, y) in enumerate(zip(xx, yy)):
#print x,y
if x < S or y < S or x + S >= W or y + S >= H:
continue
slc = slice(y - S, y + S + 1), slice(x - S, x + S + 1)
slc2 = slice(y - 3, y + 3 + 1), slice(x - 3, x + 3 + 1)
mx = np.max((II[0][slc] + II[1][slc]) / 2.)
#print 'Max within slice:', mx
#if mx > 5e3:
if mx > 2e3:
continue
mx2 = np.max((II[0][slc2] + II[1][slc2]) / 2.)
print 'Flux near object:', mx2
if mx2 < 250:
continue
#miny = np.min(Y[slc2])
#maxy = np.max(Y[slc2])
keep.append(i)
keep = np.array(keep)
if len(keep) == 0:
print 'No objects passed cuts'
return
xx = xx[keep]
yy = yy[keep]
plt.clf()
plt.imshow(X, interpolation='nearest', origin='lower', cmap='gray')
plt.title('X')
ax = plt.axis()
plt.plot(xx, yy, 'r+')
plt.plot(1596, 1452, 'o', mec=(0, 1, 0), mfc='none')
plt.axis(ax)
ps.savefig()
ylo, yhi = [], []
for i in range(min(len(xx), 100)):
x, y = xx[i], yy[i]
slc2 = slice(y - 3, y + 3 + 1), slice(x - 3, x + 3 + 1)
ylo.append(np.min(Y[slc2]))
yhi.append(np.max(Y[slc2]))
plt.clf()
plt.plot(ylo, yhi, 'r.')
plt.axis('scaled')
ps.savefig()
for i, (x, y) in enumerate(zip(xx, yy)[:50]):
print x, y
rows, cols = 2, 3
ra, dec = wcs.pixelxy2radec(x + 1, y + 1)
slc = slice(y - S, y + S + 1), slice(x - S, x + S + 1)
slc2 = slice(y - 3, y + 3 + 1), slice(x - 3, x + 3 + 1)
mx = max(np.max(II[0][slc]), np.max(II[1][slc]))
print 'Max within slice:', mx
miny = np.min(Y[slc2])
maxy = np.max(Y[slc2])
plt.clf()
plt.subplot(rows, cols, 1)
plt.imshow(II[0][slc], **ima)
plt.xticks([])
plt.yticks([])
plt.colorbar()
plt.title('epoch 1')
plt.subplot(rows, cols, 2)
plt.imshow(II[1][slc], **ima)
plt.xticks([])
plt.yticks([])
plt.colorbar()
plt.title('epoch 2')
plt.subplot(rows, cols, 3)
plt.imshow(PP[0][slc], **aa)
plt.xticks([])
plt.yticks([])
plt.colorbar()
plt.title('std 1')
plt.subplot(rows, cols, 6)
plt.imshow(PP[1][slc], **aa)
plt.xticks([])
plt.yticks([])
plt.colorbar()
plt.title('std 2')
plt.subplot(rows, cols, 4)
plt.imshow(X[slc], **aa)
plt.xticks([])
plt.yticks([])
plt.colorbar()
plt.title('X')
plt.subplot(rows, cols, 5)
plt.imshow(Y[slc], **aa)
plt.xticks([])
plt.yticks([])
plt.colorbar()
plt.title('Y')
#plt.suptitle('Tile %s, Flux: %4.0f, Range: %.2g %.2g' % (tile,mx,miny,maxy))
plt.suptitle('Tile %s, RA,Dec (%.4f, %.4f)' % (tile, ra, dec))
ps.savefig()
def kepfilter(infile,outfile,datacol,function,cutoff,passband,plot,plotlab,
clobber,verbose,logfile,status,cmdLine=False):
## startup parameters
status = 0
numpy.seterr(all="ignore")
labelsize = 24
ticksize = 16
xsize = 16
ysize = 6
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
## log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPFILTER -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'datacol='+str(datacol)+' '
call += 'function='+str(function)+' '
call += 'cutoff='+str(cutoff)+' '
call += 'passband='+str(passband)+' '
plotit = 'n'
if (plot): plotit = 'y'
call += 'plot='+plotit+ ' '
call += 'plotlab='+str(plotlab)+' '
overwrite = 'n'
if (clobber): overwrite = 'y'
call += 'clobber='+overwrite+ ' '
chatter = 'n'
if (verbose): chatter = 'y'
call += 'verbose='+chatter+' '
call += 'logfile='+logfile
kepmsg.log(logfile,call+'\n',verbose)
## start time
kepmsg.clock('KEPFILTER started at',logfile,verbose)
## test log file
logfile = kepmsg.test(logfile)
## clobber output file
if clobber: status = kepio.clobber(outfile,logfile,verbose)
if kepio.fileexists(outfile):
message = 'ERROR -- KEPFILTER: ' + outfile + ' exists. Use clobber=yes'
status = kepmsg.err(logfile,message,verbose)
## open input file
if status == 0:
instr, status = kepio.openfits(infile,'readonly',logfile,verbose)
tstart, tstop, bjdref, cadence, status = kepio.timekeys(instr,infile,logfile,verbose,status)
if status == 0:
try:
work = instr[0].header['FILEVER']
cadenom = 1.0
except:
cadenom = cadence
## fudge non-compliant FITS keywords with no values
if status == 0:
instr = kepkey.emptykeys(instr,file,logfile,verbose)
## read table structure
if status == 0:
table, status = kepio.readfitstab(infile,instr[1],logfile,verbose)
# read time and flux columns
if status == 0:
barytime, status = kepio.readtimecol(infile,table,logfile,verbose)
flux, status = kepio.readsapcol(infile,table,logfile,verbose)
# filter input data table
if status == 0:
try:
nanclean = instr[1].header['NANCLEAN']
except:
naxis2 = 0
for i in range(len(table.field(0))):
if (numpy.isfinite(barytime[i]) and numpy.isfinite(flux[i]) and flux[i] != 0.0):
table[naxis2] = table[i]
naxis2 += 1
instr[1].data = table[:naxis2]
comment = 'NaN cadences removed from data'
status = kepkey.new('NANCLEAN',True,comment,instr[1],outfile,logfile,verbose)
## read table columns
if status == 0:
intime, status = kepio.readtimecol(infile,instr[1].data,logfile,verbose)
if status == 0:
indata, status = kepio.readfitscol(infile,instr[1].data,datacol,logfile,verbose)
if status == 0:
intime = intime + bjdref
indata = indata / cadenom
## define data sampling
if status == 0:
tr = 1.0 / (cadence / 86400)
timescale = 1.0 / (cutoff / tr)
## define convolution function
if status == 0:
if function == 'boxcar':
filtfunc = numpy.ones(numpy.ceil(timescale))
elif function == 'gauss':
timescale /= 2
dx = numpy.ceil(timescale * 10 + 1)
filtfunc = kepfunc.gauss()
filtfunc = filtfunc([1.0,dx/2-1.0,timescale],linspace(0,dx-1,dx))
elif function == 'sinc':
dx = numpy.ceil(timescale * 12 + 1)
fx = linspace(0,dx-1,dx)
fx = fx - dx / 2 + 0.5
fx /= timescale
filtfunc = numpy.sinc(fx)
filtfunc /= numpy.sum(filtfunc)
## pad time series at both ends with noise model
if status == 0:
ave, sigma = kepstat.stdev(indata[:len(filtfunc)])
padded = append(kepstat.randarray(np.ones(len(filtfunc)) * ave,
np.ones(len(filtfunc)) * sigma), indata)
ave, sigma = kepstat.stdev(indata[-len(filtfunc):])
padded = append(padded, kepstat.randarray(np.ones(len(filtfunc)) * ave,
np.ones(len(filtfunc)) * sigma))
## convolve data
if status == 0:
convolved = convolve(padded,filtfunc,'same')
## remove padding from the output array
if status == 0:
if function == 'boxcar':
outdata = convolved[len(filtfunc):-len(filtfunc)]
else:
outdata = convolved[len(filtfunc):-len(filtfunc)]
## subtract low frequencies
if status == 0 and passband == 'high':
outmedian = median(outdata)
outdata = indata - outdata + outmedian
## comment keyword in output file
if status == 0:
status = kepkey.history(call,instr[0],outfile,logfile,verbose)
## clean up x-axis unit
if status == 0:
intime0 = float(int(tstart / 100) * 100.0)
if intime0 < 2.4e6: intime0 += 2.4e6
ptime = intime - intime0
xlab = 'BJD $-$ %d' % intime0
## clean up y-axis units
if status == 0:
pout = indata * 1.0
pout2 = outdata * 1.0
nrm = len(str(int(numpy.nanmax(pout))))-1
pout = pout / 10**nrm
pout2 = pout2 / 10**nrm
ylab = '10$^%d$ %s' % (nrm, plotlab)
## data limits
xmin = ptime.min()
xmax = ptime.max()
ymin = numpy.nanmin(pout)
ymax = numpy.nanmax(pout)
xr = xmax - xmin
yr = ymax - ymin
ptime = insert(ptime,[0],[ptime[0]])
ptime = append(ptime,[ptime[-1]])
pout = insert(pout,[0],[0.0])
pout = append(pout,0.0)
pout2 = insert(pout2,[0],[0.0])
pout2 = append(pout2,0.0)
## plot light curve
if status == 0 and plot:
try:
params = {'backend': 'png',
'axes.linewidth': 2.5,
'axes.labelsize': labelsize,
'axes.font': 'sans-serif',
'axes.fontweight' : 'bold',
'text.fontsize': 12,
'legend.fontsize': 12,
'xtick.labelsize': ticksize,
'ytick.labelsize': ticksize}
rcParams.update(params)
except:
print('ERROR -- KEPFILTER: install latex for scientific plotting')
status = 1
if status == 0 and plot:
pylab.figure(figsize=[xsize,ysize])
pylab.clf()
## plot filtered data
ax = pylab.axes([0.06,0.1,0.93,0.87])
pylab.gca().xaxis.set_major_formatter(pylab.ScalarFormatter(useOffset=False))
pylab.gca().yaxis.set_major_formatter(pylab.ScalarFormatter(useOffset=False))
labels = ax.get_yticklabels()
setp(labels, 'rotation', 90, fontsize=12)
pylab.plot(ptime,pout,color='#ff9900',linestyle='-',linewidth=lwidth)
fill(ptime,pout,color=fcolor,linewidth=0.0,alpha=falpha)
if passband == 'low':
pylab.plot(ptime[1:-1],pout2[1:-1],color=lcolor,linestyle='-',linewidth=lwidth)
else:
pylab.plot(ptime,pout2,color=lcolor,linestyle='-',linewidth=lwidth)
fill(ptime,pout2,color=lcolor,linewidth=0.0,alpha=falpha)
xlabel(xlab, {'color' : 'k'})
ylabel(ylab, {'color' : 'k'})
xlim(xmin-xr*0.01,xmax+xr*0.01)
if ymin >= 0.0:
ylim(ymin-yr*0.01,ymax+yr*0.01)
else:
ylim(1.0e-10,ymax+yr*0.01)
pylab.grid()
# render plot
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
## write output file
if status == 0:
for i in range(len(outdata)):
instr[1].data.field(datacol)[i] = outdata[i]
instr.writeto(outfile)
## close input file
if status == 0:
status = kepio.closefits(instr,logfile,verbose)
## end time
if (status == 0):
message = 'KEPFILTER completed at'
else:
message = '\nKEPFILTER aborted at'
kepmsg.clock(message,logfile,verbose)
def fit_exp(o_xdata,o_ydata,o_yerr):
import scipy, pylab
a = scipy.array(o_ydata)
a, b, varp = pylab.hist(a,bins=scipy.arange(-2,2,0.05))
pylab.xlabel("shear")
pylab.ylabel("Number of Galaxies")
#pylab.show()
o_xdata = scipy.array(o_xdata)
o_ydata = scipy.array(o_ydata)
o_yerr = scipy.array(o_yerr)
print o_yerr
#o_xdata = o_xdata[abs(o_ydata) > 0.05]
#o_yerr = o_yerr[abs(o_ydata) > 0.05]
#o_ydata = o_ydata[abs(o_ydata) > 0.05]
both = 0
As = []
for z in range(25):
xdata = []
ydata = []
yerr = []
for i in range(len(o_xdata)):
rand = int(random.random()*len(o_xdata)) - 1
#print rand, len(o_xdata)
xdata.append(o_xdata[rand])
ydata.append(o_ydata[rand])
yerr.append(o_yerr[rand])
xdata = scipy.array(xdata)
ydata = scipy.array(ydata)
##########
# Fitting the data -- Least Squares Method
##########
# Power-law fitting is best done by first converting
# to a linear equation and then fitting to a straight line.
#
# y = a * x^b
# log(y) = log(a) + b*log(x)
#
powerlaw = lambda x, amp, index: amp * (x**index)
#print xdata
#print ydata
ydata = ydata / (scipy.ones(len(ydata)) + abs(ydata))
# define our (line) fitting function
#fitfunc = lambda p, x: p[0]*x**p[1]
if both:
fitfunc = lambda p, x: p[0]*x**p[1]
errfunc = lambda p, x, y, err: (y - fitfunc(p, x)) / err
pinit = [1.,-1.]
else:
fitfunc = lambda p, x: p[0]*x**-1.
errfunc = lambda p, x, y, err: (y - fitfunc(p, x)) / err
pinit = [1.] #, -1.0]
#ydataerr = scipy.ones(len(ydata)) * 0.3
out = scipy.optimize.leastsq(errfunc, pinit, args=(scipy.array(xdata), scipy.array(ydata), scipy.array(yerr)), full_output=1)
if both:
pfinal = out[0]
covar = out[1]
print pfinal
print covar
index = pfinal[1]
amp = pfinal[0]
ampErr = covar[0][0]
indexErr = covar[1][1]
else:
pfinal = out[0]
covar = out[1]
print pfinal
print covar
index = -1. #pfinal[1]
amp = pfinal #[0]
ampErr = covar[0][0]**0.5
indexErr = 0 #covar
#indexErr = scipy.sqrt( covar[0][0] )
#ampErr = scipy.sqrt( covar[1][1] ) * amp
##########
# Plotting data
##########
import pylab
pylab.clf()
#pylab.subplot(2, 1, 1)
pylab.errorbar(xdata, ydata, yerr=yerr, fmt='k.') # Data
from copy import copy
xdataline = copy(xdata)
xdataline.sort()
pylab.plot(xdataline, powerlaw(xdataline, amp, index)) # Fit
pylab.text(5, 6.5, 'Ampli = %5.2f +/- %5.2f' % (amp, ampErr))
pylab.text(5, 5.5, 'Index = %5.2f +/- %5.2f' % (index, indexErr))
pylab.title('Best Fit Power Law')
pylab.xlabel('X')
pylab.ylabel('Y')
#pylab.subplot(2, 1, 2)
#pylab.loglog(xdataline, powerlaw(xdataline, amp, index))
#pylab.errorbar(xdata, ydata, yerr=ydataerr, fmt='k.') # Data
#pylab.xlabel('X (log scale)')
#pylab.ylabel('Y (log scale)')
#pylab.xlim(1.0, 11)
print z
if both:
pylab.show()
#pylab.show()
pylab.clf()
As.append(amp)
As = scipy.array(As)
return As.mean(), As.std()
mySamples = []
myLinear = []
myQuadratic = []
myCubic = []
myExponential = []
for i in range(0, 30):
mySamples.append(i)
myLinear.append(i)
myQuadratic.append(i**2)
myCubic.append(i**3)
myExponential.append(1.4**i)
# Generate linear vs quadratic plot
plt.figure("lin quad")
plt.clf() # clears the frame
plt.ylim(0, 1000)
plt.plot(mySamples, myLinear, "b-", label="linear") # b- means blue line
plt.plot(mySamples, myQuadratic, "ko",
label="quadratic") # ko means black dots
plt.legend(
loc="upper right"
) # specifies the location of the legend instead of applying pylab default
# Generate cubic vs exponential plot
plt.figure("cube exp")
plt.clf() # clears the frame
plt.plot(mySamples, myCubic, "r--", label="cubic") # r-- means red dashed
plt.plot(mySamples, myExponential, "g^",
label="exponential") # g^ means green triangles
plt.legend() # apply pylab default for legend location
def plot_compare_methods(offsets,
eoffsets,
dx=None,
dy=None,
fig1=1,
fig2=2,
legend=True):
"""
plot wrapper
"""
import pylab
pylab.figure(fig1)
pylab.clf()
if dx is not None and dy is not None:
pylab.plot([dx], [dy],
'kx',
markersize=30,
zorder=50,
markeredgewidth=3)
pylab.errorbar(offsets[:, 0],
offsets[:, 1],
xerr=eoffsets[:, 0],
yerr=eoffsets[:, 1],
linestyle='none',
label='DFT')
pylab.errorbar(offsets[:, 2],
offsets[:, 3],
xerr=eoffsets[:, 2],
yerr=eoffsets[:, 3],
linestyle='none',
label='Taylor')
pylab.errorbar(offsets[:, 4],
offsets[:, 5],
xerr=eoffsets[:, 4],
yerr=eoffsets[:, 5],
linestyle='none',
label='Gaussian')
pylab.errorbar(offsets[:, 6],
offsets[:, 7],
xerr=eoffsets[:, 6],
yerr=eoffsets[:, 7],
linestyle='none',
label='$\\chi^2$')
if legend:
pylab.legend(loc='best')
means = offsets.mean(axis=0)
stds = offsets.std(axis=0)
emeans = eoffsets.mean(axis=0)
estds = eoffsets.std(axis=0)
print("Standard Deviations: ", stds)
print("Error Means: ", emeans)
print("emeans/stds: ", emeans / stds)
pylab.figure(fig2)
pylab.clf()
if dx is not None and dy is not None:
pylab.plot([dx], [dy],
'kx',
markersize=30,
zorder=50,
markeredgewidth=3)
pylab.errorbar(means[0],
means[1],
xerr=emeans[0],
yerr=emeans[1],
capsize=20,
color='r',
dash_capstyle='round',
solid_capstyle='round',
label='DFT')
pylab.errorbar(means[2],
means[3],
xerr=emeans[2],
yerr=emeans[3],
capsize=20,
color='g',
dash_capstyle='round',
solid_capstyle='round',
label='Taylor')
pylab.errorbar(means[4],
means[5],
xerr=emeans[4],
yerr=emeans[5],
capsize=20,
color='b',
dash_capstyle='round',
solid_capstyle='round',
label='Gaussian')
pylab.errorbar(means[6],
means[7],
xerr=emeans[6],
yerr=emeans[7],
capsize=20,
color='m',
dash_capstyle='round',
solid_capstyle='round',
label='$\\chi^2$')
pylab.errorbar(means[0],
means[1],
xerr=stds[0],
yerr=stds[1],
capsize=10,
color='r',
linestyle='--',
linewidth=5)
pylab.errorbar(means[2],
means[3],
xerr=stds[2],
yerr=stds[3],
capsize=10,
color='g',
linestyle='--',
linewidth=5)
pylab.errorbar(means[4],
means[5],
xerr=stds[4],
yerr=stds[5],
capsize=10,
color='b',
linestyle='--',
linewidth=5)
pylab.errorbar(means[6],
means[7],
xerr=stds[6],
yerr=stds[7],
capsize=10,
color='m',
linestyle='--',
linewidth=5)
if legend:
pylab.legend(loc='best')
def epoch_coadd_plots(tractor, ps, S, ima, yearcut, fakewcs):
bimg = np.zeros((S, S))
bmod = np.zeros((S, S))
bnum = np.zeros((S, S))
bchisq = np.zeros((S, S))
bchi = np.zeros((S, S))
aimg = np.zeros((S, S))
amod = np.zeros((S, S))
anum = np.zeros((S, S))
achisq = np.zeros((S, S))
achi = np.zeros((S, S))
tims = tractor.getImages()
for i, tim in enumerate(tims):
mod = tractor.getModelImage(i)
hh, ww = tim.shape
wrap = TractorWCSWrapper(tim.wcs, ww, hh)
#print 'Shape', tim.shape
#print 'WCS', tim.wcs
#print 'WCS', tim.wcs.wcs
Yo, Xo, Yi, Xi, [rim,
rmod] = resample_with_wcs(fakewcs, wrap,
[tim.data, mod], 3)
if tim.time.toYear() > yearcut:
im, mod, num, chisq, chi = (aimg, amod, anum, achisq, achi)
else:
im, mod, num, chisq, chi = (bimg, bmod, bnum, bchisq, bchi)
im[Yo, Xo] += rim
mod[Yo, Xo] += rmod
num[Yo, Xo] += 1.
chi[Yo, Xo] += ((rim - rmod) * tim.getInvError()[Yi, Xi])
chisq[Yo, Xo] += ((rim - rmod)**2 * tim.getInvvar()[Yi, Xi])
bimg /= np.maximum(bnum, 1)
aimg /= np.maximum(anum, 1)
bmod /= np.maximum(bnum, 1)
amod /= np.maximum(anum, 1)
#print 'N', anum.max(), bnum.max()
#print 'mean N', anum.mean(), bnum.mean()
achi /= np.maximum(anum, 1)
bchi /= np.maximum(bnum, 1)
nn = np.mean([anum.mean(), bnum.mean()])
#chimax = max(achisq.max(), bchisq.max())
#ca = dict(interpolation='nearest', origin='lower', vmin=0, vmax=chimax)
c2a = dict(interpolation='nearest', origin='lower', vmin=0, vmax=16 * nn)
ca = dict(interpolation='nearest', origin='lower', vmin=-3, vmax=3)
plt.clf()
plt.subplot(2, 3, 1)
plt.imshow(bimg, **ima)
plt.subplot(2, 3, 2)
plt.imshow(bmod, **ima)
plt.title('First epoch')
plt.subplot(2, 3, 3)
#plt.imshow(bchisq, **c2a)
plt.imshow(bchi, **ca)
plt.subplot(2, 3, 4)
plt.imshow(aimg, **ima)
plt.subplot(2, 3, 5)
plt.imshow(amod, **ima)
plt.title('Second epoch')
plt.subplot(2, 3, 6)
#plt.imshow(achisq, **c2a)
plt.imshow(achi, **ca)
ps.savefig()
def tests():
x = pylab.arange(0.0, 2 * pylab.pi, 0.01)
list_y = (pylab.sin(x), pylab.sin(2 * x))
plot_and_format((x, ), (list_y[0], ))
exportplot('test/test1_one_curve.png')
pylab.clf()
list_x = (x, x)
plot_and_format(list_x, list_y)
exportplot('test/test2_two_curves.png')
pylab.clf()
list_format = ('k-', 'r--')
plot_and_format(list_x, list_y, list_format=list_format)
exportplot('test/test3_two_curves_formatting.png')
pylab.clf()
plot_and_format(list_x,
list_y,
list_format=list_format,
xlabel='hello x axis')
exportplot('test/test4_two_curves_formatting_xlab.png')
pylab.clf()
plot_and_format(list_x,
list_y,
list_format=list_format,
legend=['sin($x$)', 'sin($2x$)'])
exportplot('test/test5_two_curves_formatting_legend.png')
pylab.clf()
plot_and_format(list_x,
list_y,
list_format=list_format,
xticks={
'ticks': [0, pylab.pi, 2 * pylab.pi],
'labels': ['0', '$\pi$', '$2\pi$']
})
exportplot('test/test6_two_curves_formatting_xticks.png')
pylab.clf()
plot_and_format(list_x,
list_y,
list_format=list_format,
xticks={
'ticks': [0, pylab.pi, 2 * pylab.pi],
'labels': ['0', '$\pi$', '$2\pi$']
},
xlim=[0, 2 * pylab.pi])
exportplot('test/test7_two_curves_formatting_xticks_xlim.png')
pylab.clf()
def perceptron(hidden_neurons=5, weightdecay=0.01, momentum=0.1):
INPUT_FEATURES = 2
CLASSES = 3
HIDDEN_NEURONS = hidden_neurons
WEIGHTDECAY = weightdecay
MOMENTUM = momentum
# Generate the labeled set
g = generate_data()
#g = generate_data2()
alldata = g['d']
minX, maxX, minY, maxY = g['minX'], g['maxX'], g['minY'], g['maxY']
# Split data into test and training dataset
tstdata, trndata = alldata.splitWithProportion(0.25)
trndata._convertToOneOfMany() # This is necessary, but I don't know why
tstdata._convertToOneOfMany() # http://stackoverflow.com/q/8154674/562769
print("Number of training patterns: %i" % len(trndata))
print("Input and output dimensions: %i, %i" %
(trndata.indim, trndata.outdim))
print("Hidden neurons: %i" % HIDDEN_NEURONS)
print("First sample (input, target, class):")
print(trndata['input'][0], trndata['target'][0], trndata['class'][0])
fnn = buildNetwork(trndata.indim,
HIDDEN_NEURONS,
trndata.outdim,
outclass=SoftmaxLayer)
trainer = BackpropTrainer(fnn,
dataset=trndata,
momentum=MOMENTUM,
verbose=True,
weightdecay=WEIGHTDECAY)
# Visualization
ticksX = arange(minX - 1, maxX + 1, 0.2)
ticksY = arange(minY - 1, maxY + 1, 0.2)
X, Y = meshgrid(ticksX, ticksY)
# need column vectors in dataset, not arrays
griddata = ClassificationDataSet(INPUT_FEATURES, 1, nb_classes=CLASSES)
for i in range(X.size):
griddata.addSample([X.ravel()[i], Y.ravel()[i]], [0])
for i in range(20):
trainer.trainEpochs(1)
trnresult = percentError(trainer.testOnClassData(), trndata['class'])
tstresult = percentError(trainer.testOnClassData(dataset=tstdata),
tstdata['class'])
print("epoch: %4d" % trainer.totalepochs,
" train error: %5.2f%%" % trnresult,
" test error: %5.2f%%" % tstresult)
out = fnn.activateOnDataset(griddata)
# the highest output activation gives the class
out = out.argmax(axis=1)
out = out.reshape(X.shape)
figure(1) # always print on the same canvas
ioff() # interactive graphics off
clf() # clear the plot
for c in [0, 1, 2]:
here, _ = where(tstdata['class'] == c)
plot(tstdata['input'][here, 0], tstdata['input'][here, 1], 'o')
if out.max() != out.min(): # safety check against flat field
contourf(X, Y, out) # plot the contour
ion() # interactive graphics on
draw() # update the plot
ioff()
show()
def __call__(
self,
model=None,
name=None,
fignum=5,
axes=None,
axis=None, #(1e2,1e6,1e-7,1e-2),
data_kwargs=dict(
linewidth=2,
color='k',
),
fit_kwargs=dict(
lw=2,
color='r',
),
butterfly=True,
outdir=None,
suffix='_sed',
galmap=None,
annotate=None,
grid=True,
):
"""Plot the SED
======== ===================================================
keyword description
======== ===================================================
model spectral model object
name name of the source
fignum [5] if set, use (and clear) this figure. If None, use current Axes object
axes [None] If set use this Axes object
axis None, (1e2, 1e5, 1e-8, 1e-2) depending on energy flux unit
data_kwargs a dict to pass to the data part of the display
fit_kwargs a dict to pass to the fit part of the display
butterfly [True] plot model with a butterfly outline
outdir [None] if set, save sed into <outdir>/<source_name>_sed.png if outdir is a directory, save into filename=<outdir> if noself.
suffix ['_sed'] Add to source name to form filename
galmap [None] if set to a SkyDir, create a little galactic map showing this position
annotate [None] if set, a tuple of (x, y, text), in axes coords
grid [True] Set False to turn off grid
======== ===================================================
"""
if model is None: model = self.model
if name is None: name = self.name
energy_flux_factor = self.scale_factor
# conversion 1.602E-19 * 1E6 eV/Mev * 1E7 erg/J * = 1.602E-6 erg/MeV
oldlw = plt.rcParams['axes.linewidth']
oldticksize = plt.rcParams['xtick.labelsize']
plt.rcParams['axes.linewidth'] = 2
plt.rcParams['xtick.labelsize'] = plt.rcParams['ytick.labelsize'] = 10
if axes is None:
fig = plt.figure(fignum, figsize=(4, 4))
plt.clf()
fig.add_axes((0.22, 0.15, 0.75, 0.72))
axes = plt.gca()
self.axes = axes
axes.set_xscale('log')
axes.set_yscale('log')
if axis is None:
axis = (1e2, 4e5, 0.2 * self.scale_factor, 1e4 * self.scale_factor)
axes.axis(axis)
axes.grid(grid)
axes.set_autoscale_on(False)
self.plot_data(axes, **data_kwargs)
# and the model, perhaps with a butterfly
self.dom = np.logspace(np.log10(self.rec.elow[0]),
np.log10(self.rec.ehigh[-1]), 26)
self.plot_model(model, butterfly, **fit_kwargs)
plt.rcParams['axes.linewidth'] = oldlw
plt.rcParams['xtick.labelsize'] = plt.rcParams[
'ytick.labelsize'] = oldticksize
# the axis labels (note reduced labelpad for y)
axes.set_ylabel(r'$\mathsf{Energy\ Flux\ (%s\ cm^{-2}\ s^{-1})}$' %
self.energy_flux_unit,
labelpad=0)
axes.set_xlabel(r'$\mathsf{Energy\ (GeV)}$')
if self.energy_flux_unit == 'eV':
axes.set_yticklabels(
['', '1', '10', '100', r'$\mathdefault{10^{3}}$'])
axes.set_title(name, size=14)
set_xlabels(axes, self.gev_scale)
# add a galactic map if requested
if galmap is not None:
image.galactic_map(galmap,
axes=self.axes,
color='lightblue',
marker='s',
markercolor='r',
markersize=20)
if annotate is not None:
axes.text(annotate[0],
annotate[1],
annotate[2],
transform=axes.transAxes,
fontsize=8)
if outdir is not None:
self.name = name
self.savefig(outdir, suffix)
def addLiteMapsWithSpectralWeighting(liteMap1,
liteMap2,
kMask1Params=None,
kMask2Params=None,
signalMap=None):
"""
@brief add two maps, weighting in Fourier space
Maps must be the same size.
@param kMask1Params mask params for liteMap1 (see fftTools.power2D.createKspaceMask)
@param kMask2Params mask params for liteMap2 (see fftTools.power2D.createKspaceMask)
@param signalMap liteMap with best estimate of signal to use when estimating noise weighting
@return new map
"""
#Get fourier weights
flTrace.issue("liteMap", 0, "Computing Weights")
#np1 = fftTools.noisePowerFromLiteMaps(liteMap1, liteMap2, applySlepianTaper = False)
#np2 = fftTools.noisePowerFromLiteMaps(liteMap2, liteMap1, applySlepianTaper = False)
data1 = copy.copy(liteMap1.data)
data2 = copy.copy(liteMap2.data)
if signalMap != None:
liteMap1.data[:] = (liteMap1.data - signalMap.data)[:]
liteMap2.data[:] = (liteMap2.data - signalMap.data)[:]
np1 = fftTools.powerFromLiteMap(liteMap1) #, applySlepianTaper = True)
np2 = fftTools.powerFromLiteMap(liteMap2) #), applySlepianTaper = True)
print "testing", liteMap1.data == data1
liteMap1.data[:] = data1[:]
liteMap2.data[:] = data2[:]
n1 = np1.powerMap
n2 = np2.powerMap
# n1[np.where( n1<n1.max()*.002)] = n1.max()*.001
# n2[np.where( n2<n2.max()*.002)] = n2.max()*.001
w1 = 1 / n1
w2 = 1 / n2
m1 = np.median(w1)
m2 = np.median(w2)
w1[np.where(abs(w1) > 4 * m1)] = 4 * m1
w2[np.where(abs(w2) > 4 * m2)] = 4 * m2
#w1[:] = 1.
#w2[:] = 1.
#pylab.hist(w1.ravel())
#pylab.savefig("hist1.png")
#pylab.clf()
yrange = [4, 5000]
np1.powerMap = w1
#np1.plot(pngFile="w1.png", log=True, zoomUptoL=8000, yrange = yrange)
np2.powerMap = w2
#np2.plot(pngFile="w2.png", log=True, zoomUptoL=8000, yrange = yrange)
if kMask1Params != None:
np1.createKspaceMask(**kMask1Params)
w1 *= np1.kMask
if kMask2Params != None:
np2.createKspaceMask(**kMask2Params)
w2 *= np2.kMask
pylab.clf()
invW = 1.0 / (w1 + w2)
invW[np.where(np.isnan(invW))] = 0.
invW[np.where(np.isinf(invW))] = 0.
flTrace.issue("liteMap", 3,
"NaNs in inverse weight: %s" % str(np.where(np.isnan(invW))))
flTrace.issue("liteMap", 3,
"Infs in inverse weight: %s" % str(np.where(np.isinf(invW))))
flTrace.issue("liteMap", 2, "Adding Maps")
f1 = fftTools.fftFromLiteMap(liteMap1, applySlepianTaper=False)
f2 = fftTools.fftFromLiteMap(liteMap2, applySlepianTaper=False)
kTot = (f1.kMap * w1 + f2.kMap * w2) * invW
flTrace.issue(
"liteMap", 3,
"NaNs in filtered transform: %s" % str(np.where(np.isnan(kTot))))
f1.kMap = kTot
finalMap = liteMap1.copy()
finalMap.data[:] = 0.
finalMap.data = f1.mapFromFFT()
return finalMap
