def fast_CIC_deposit(x, mi, Ngrid=N, periodic=1):
"""cloud in cell density estimator
"""
if ((np.size(mi)) < (np.size(x))):
m = x.copy()
m[:] = mi
else:
m = mi
dx = 1. / Ngrid
rho = np.zeros(Ngrid)
left = x - 0.5 * dx
right = left + dx
xi = np.int32(left / dx)
frac = (1. + xi - left / dx)
ind = pyl.where(left < 0.)
frac[ind] = (-(left[ind] / dx))
xi[ind] = Ngrid - 1
xir = xi.copy() + 1
xir[xir == Ngrid] = 0
rho = pyl.bincount(xi, weights=frac * m, minlength=Ngrid)
rho2 = pyl.bincount(xir, weights=(1. - frac) * m, minlength=Ngrid)
rho += rho2
return rho * Ngrid
def OutToClass(outputs, targets):
outs = []
trgs = []
for out, trg in zip(outputs, targets):
# this is to have each output neruon responsible for a class
# if False and len(out) == 3 and \
if len(out) == 1:
outs.append(out[0])
trgs.append(trg[0])
# print out[0]
elif len(out) == 3 and \
array([where(x in [1, 0], True, False) for x in out]).all() and \
bincount(out.astype('int'))[0] != 2:
outs.append(-1)
trgs.append(argmax(trg))
else:
outs.append(argmax(out))
trgs.append(argmax(trg))
return outs, trgs
def OutToClass(outputs, targets):
outs = []
trgs = []
for out, trg in zip(outputs, targets):
# this is to have each output neruon responsible for a class
# if False and len(out) == 3 and \
if len(out) == 1:
outs.append(out[0])
trgs.append(trg[0])
# print out[0]
elif len(out) == 3 and \
array([where(x in [1, 0], True, False) for x in out]).all() and \
bincount(out.astype('int'))[0] != 2:
outs.append(-1)
trgs.append(argmax(trg))
else:
outs.append(argmax(out))
trgs.append(argmax(trg))
return outs, trgs
def testOutput(self):
self.assertEqual(bincount(self.net2.ao.astype('int'))[0],
2)
self.assertEqual(bincount(self.net2.ao.astype('int'))[1],
1)
def classify(self, x):
d = self.X - tile(x.reshape(self.n, 1), self.N)
dsq = sum(d*d, 0)
neighbours = self.c[argpartition(dsq, self.k)[:self.k]]
most_common = argmax(bincount(neighbours.astype(int)))
return most_common
zspec = pylab.array(zspec) zphot = pylab.array(zphot) lmass = pylab.array(lmass) zlss = pylab.array(zlss) dzspec = (zspec - zlss) / (1 + zspec) dzphot = (zphot - zlss) / (1 + zphot) ### binning by mass digi_truepos = pylab.digitize(lmass[inds_truepos], lmassbins) digi_trueneg = pylab.digitize(lmass[inds_trueneg], lmassbins) digi_falsepos = pylab.digitize(lmass[inds_falsepos], lmassbins) digi_falseneg = pylab.digitize(lmass[inds_falseneg], lmassbins) bincount_truepos = pylab.bincount(digi_truepos, minlength=len(lmassbins)+1)[1:-1] bincount_trueneg = pylab.bincount(digi_trueneg, minlength=len(lmassbins)+1)[1:-1] bincount_falsepos = pylab.bincount(digi_falsepos, minlength=len(lmassbins)+1)[1:-1] bincount_falseneg = pylab.bincount(digi_falseneg, minlength=len(lmassbins)+1)[1:-1] n_truepos[i] += bincount_truepos n_trueneg[i] += bincount_trueneg n_falsepos[i] += bincount_falsepos n_falseneg[i] += bincount_falseneg print 'done with +/- 1.5 sigma_zphot' nhinlo_falsepos_tot = pylab.array([mypy.massfunc.confidence_interval(ni) for ni in n_falsepos.sum(axis=0)])
(f.cat.z_spec[f.inds_spatial] > zlo_spec) & (f.cat.z_spec[f.inds_spatial] < zhi_spec)) ### LSS candidates selected by zphot members_zphot = pylab.find((f.cat.use[f.inds_spatial] == 1) & (f.cat.z_spec[f.inds_spatial] < 0) & (dr_pkpc_min[f.inds_spatial] <= 1500.) & (f.fout.z[f.inds_spatial] > zlo_phot) & (f.fout.z[f.inds_spatial] < zhi_phot)) ### binning galaxies by stellar mass digi_mass_zspec = pylab.digitize(f.fout.lmass[f.inds_spatial][members_zspec], lmassbins) digi_mass_zphot = pylab.digitize(f.fout.lmass[f.inds_spatial][members_zphot], lmassbins) ngal_bins_zspec = pylab.bincount(digi_mass_zspec, minlength=len(lmassbins)+1)[1:-1] ngal_bins_zphot = pylab.bincount(digi_mass_zphot, minlength=len(lmassbins)+1)[1:-1] ngal_bins_zphot_corr = ngal_bins_zphot * corr_factor nfinal[i] += ngal_bins_zspec + ngal_bins_zphot_corr ################### ### STAR-FORMING ################### ### LSS members selected by zspec members_zspec_sf = pylab.find((f.cat.use[f.inds_spatial] == 1) &
def GetGS(image_name, scale, roi=None, show=True, min_size=500, exclude_zones=None, flipudflag=False):
# Load image (Rappel pour convertir couleur to rgb color.rgb2gray)
if opencv:
original = cv2.imread(image_name)
else:
original = m.imread(image_name)
if flipudflag:
original = flipud(original)
# manage exclusion zone put them to 1 i.e. bottom
if exclude_zones != None:
# create markers of background and gravel
markers_zones = m.zeros_like(original[:, :, 0])
for zone in exclude_zones:
xa = min(zone[0], zone[2])
xb = max(zone[0], zone[2])
ya = min(zone[1], zone[3])
yb = max(zone[1], zone[3])
markers_zones[ya:yb, xa:xb] = 1
if roi != None:
# crop the image
xa = min(roi[0], roi[2])
xb = max(roi[0], roi[2])
ya = min(roi[1], roi[3])
yb = max(roi[1], roi[3])
original = original[ya:yb, xa:xb]
if exclude_zones != None:
markers_zones = markers_zones[ya:yb, xa:xb]
# transform to hsv
if opencv:
img = cv2.cvtColor(original, cv2.COLOR_BGR2HSV)
else:
img = color.rgb2hsv(original)
# use s chanel
img = img[:, :, 1]
# div by 255 si en couleur
thre = img
if show:
m.figure()
m.imshow(original)
# test filtre sobel (avoir les pentes)
if opencv:
elev = cv2.Laplacian(thre, cv2.CV_64F)
else:
elev = filters.sobel(thre)
# compute an auto threshold
thresh = filters.threshold_otsu(thre)
# create markers of background and gravel
markers = m.zeros_like(thre)
if show:
print thresh
markers[thre < thresh] = 2
markers[thre > thresh] = 1
if exclude_zones != None:
markers[markers_zones == 1] = 1
# use watershade transform (use markes as starting point)
segmentation = morphology.watershed(elev, markers)
# Clean small object
if opencv:
kernel = m.ones((2, 2), m.uint8)
closing = cv2.morphologyEx(segmentation - 1, cv2.MORPH_CLOSE, kernel)
else:
closing = ndimage.binary_closing(segmentation - 1)
tmp = ndimage.binary_fill_holes(closing)
label_objects, nb_labels = ndimage.label(tmp)
sizes = m.bincount(label_objects.ravel())
mask_sizes = sizes > min_size
mask_sizes[0] = 0
segmentation_cleaned = mask_sizes[label_objects]
# relabel cleaned version of segmentation
label_objects_clean, nb_label_clean = ndimage.label(segmentation_cleaned)
# plot contour of object
if show:
m.contour(ndimage.binary_fill_holes(label_objects_clean), linewidths=1.2, colors="y")
# trouve les informations des objets
# old version of scikit properties=measurement_types
mes = measure.regionprops(label_objects_clean)
granulo = []
for prop in mes:
# Correct orientation ! car orientation prend pas en compte le cadrant !!!
#: elements of the inertia tensor [a b; b c]
Orientation = GetOrientation(prop["CentralMoments"])
x0 = prop["Centroid"][1]
y0 = prop["Centroid"][0]
x1 = x0 + m.cos(Orientation) * 0.5 * prop["MajorAxisLength"]
y1 = y0 - m.sin(Orientation) * 0.5 * prop["MajorAxisLength"]
x2 = x0 - m.sin(Orientation) * 0.5 * prop["MinorAxisLength"]
y2 = y0 - m.cos(Orientation) * 0.5 * prop["MinorAxisLength"]
if show:
m.plot((x0, x1), (y0, y1), "-r", linewidth=2.5)
m.plot((x0, x2), (y0, y2), "-r", linewidth=2.5)
m.plot(x0, y0, ".g", markersize=15)
granulo.append(prop["MinorAxisLength"] / scale)
# minr, minc, maxr, maxc = prop['BoundingBox']
# bx = (minc, maxc, maxc, minc, minc)
# by = (minr, minr, maxr, maxr, minr)[
# m.plot(bx, by, '-b', linewidth=2.5)
return m.array(granulo), label_objects_clean, mes
### calculating MFs
dm = 0.25
lmassbins = pylab.arange(9.5 - dm / 2., 11.5 + dm, dm)
lmassbars = (lmassbins[1:] + lmassbins[:-1]) / 2.
xlo, xhi = 25. * 100. / dx_map, 100 - 25. * 100. / dx_map
ylo, yhi = 25. * 100. / dy_map, 100 - 25. * 100. / dy_map
inds0 = pylab.find((overdens_arr > 0.0) & (overdens_arr < 0.5)
& (simdata.x_cMpc > xlo) & (simdata.x_cMpc < xhi)
& (simdata.y_cMpc > ylo) & (simdata.y_cMpc < yhi))
inds1 = pylab.find((overdens_arr > 0.5) & (overdens_arr < 1.0)
& (simdata.x_cMpc > xlo) & (simdata.x_cMpc < xhi)
& (simdata.y_cMpc > ylo) & (simdata.y_cMpc < yhi))
inds2 = pylab.find((overdens_arr > 1.0) & (overdens_arr < 1.5)
& (simdata.x_cMpc > xlo) & (simdata.x_cMpc < xhi)
& (simdata.y_cMpc > ylo) & (simdata.y_cMpc < yhi))
inds3 = pylab.find((overdens_arr > 1.5) & (overdens_arr < 2.0)
& (simdata.x_cMpc > xlo) & (simdata.x_cMpc < xhi)
& (simdata.y_cMpc > ylo) & (simdata.y_cMpc < yhi))
digi0 = pylab.digitize(pylab.log10(simdata.stellarMass[inds0]), lmassbins)
digi1 = pylab.digitize(pylab.log10(simdata.stellarMass[inds1]), lmassbins)
digi2 = pylab.digitize(pylab.log10(simdata.stellarMass[inds2]), lmassbins)
digi3 = pylab.digitize(pylab.log10(simdata.stellarMass[inds3]), lmassbins)
ngal0 = pylab.bincount(digi0, minlength=len(lmassbins) + 1)[1:-1]
ngal1 = pylab.bincount(digi1, minlength=len(lmassbins) + 1)[1:-1]
ngal2 = pylab.bincount(digi2, minlength=len(lmassbins) + 1)[1:-1]
ngal3 = pylab.bincount(digi3, minlength=len(lmassbins) + 1)[1:-1]
def testOutput(self):
self.assertEqual(bincount(self.net2.ao.astype('int'))[0], 2)
self.assertEqual(bincount(self.net2.ao.astype('int'))[1], 1)
& (f.fout.z[f.inds_spatial] < zhi))
subinds_massive = pylab.find((f.cat.use[f.inds_spatial] == 1)
& (f.fout.z[f.inds_spatial] > zlo)
& (f.fout.z[f.inds_spatial] < zhi)
& (f.fout.lmass[f.inds_spatial] > 11))
if 0.19 < zlo < 0.76:
for si in subinds_massive:
s[fi] += ' mugshot_%05i_%s.pdf' % (
f.cat.id[f.inds_spatial][si], f.version)
digi_mass = pylab.digitize(f.fout.lmass[f.inds_spatial][subinds],
massbins)
ngal_bins = pylab.bincount(digi_mass,
minlength=len(massbins) + 1)[1:-1]
nlo_poisson, nhi_poisson = [], []
for n in ngal_bins:
nhi, nlo = mypy.massfunc.confidence_interval(n)
nlo_poisson.append(nlo)
nhi_poisson.append(nhi)
nlo_poisson, nhi_poisson = pylab.array(nlo_poisson), pylab.array(
nhi_poisson)
phi_bins = ngal_bins * 1. / volume / dm
ephi_lo = phi_bins * nlo_poisson / ngal_bins
ephi_lo[pylab.isnan(ephi_lo)] = 0
ephi_hi = phi_bins * nhi_poisson / ngal_bins
ephi_hi[pylab.isnan(ephi_hi)] = (
1. / volume / dm) * nhi_poisson[pylab.isnan(ephi_hi)] / 1.
#! /usr/bin/env python
import sys, pylab
x = 5**5**5
t = '$5^{5^5}$'
l = pylab.fromstring(str(x), dtype='uint8') - 48 #Remove ASCII 0 offset
bin_var = pylab.arange(10)
bin_cnt = pylab.bincount(l, minlength=10).astype('double')
bin_cnt /= bin_cnt.sum()
bin_cnt -= bin_cnt.mean()
bin_srt = bin_cnt.argsort()
pylab.figure(1)
pylab.barh(bin_var, bin_cnt[bin_srt], align='center')
pylab.yticks(bin_var, bin_srt)
pylab.axis(ymin=-0.5, ymax=9.5)
pylab.axvline(0)
pylab.ylabel(r'Decimal Digits (sorted by frequency)')
pylab.xlabel(r'Mean Centred Normalised Frequency')
pylab.title(r'%s is %d decimal digits long' % (t, len(l)))
pylab.grid(True)
pylab.savefig('long.png')
pylab.show()
