def shapelet_getroot(xfn, yfn, xco, xcen, ycen):
""" This finds the root for finding the shapelet centre. If there are multiple roots, takes
that which closest to the 'centre', taken as the intensity barycentre. This is the python
version of getroot.f of anaamika."""
import functions as func
root = None
npoint = len(xfn)
error = 0
if npoint == 0:
error = 1
elif yfn.max() * yfn.min() >= 0.:
error = 1
minint = 0
minintold = 0
for i in range(1, npoint):
if yfn[i - 1] * yfn[i] < 0.:
if minintold == 0: # so take nearest to centre
if abs(yfn[i - 1]) < abs(yfn[i]):
minint = i - 1
else:
minint = i
else:
dnew = func.dist_2pt([xco, xfn[i]], [xcen, ycen])
dold = func.dist_2pt([xco, xfn[minintold]], [xcen, ycen])
if dnew <= dold:
minint = i
else:
minint = minintold
minintold = minint
if minint < 1 or minint > npoint: error = 1
if error != 1:
low = minint - min(2, minint) #-1)
up = minint + min(2,
npoint - 1 - minint) # python array indexing rubbish
nfit = up - low + 1
xfit = xfn[low:low + nfit]
yfit = yfn[low:low + nfit]
sig = N.ones(nfit)
smask = N.zeros(nfit, dtype=bool)
xx = [i for i in range(low, low + nfit)]
[c, m], errors = func.fit_mask_1d(xfit,
yfit,
sig,
smask,
func.poly,
do_err=False,
order=1)
root = -c / m
if root < xfn[low] or root > xfn[up]: error = 1
return root, error
def shapelet_getroot(xfn, yfn, xco, xcen, ycen):
""" This finds the root for finding the shapelet centre. If there are multiple roots, takes
that which closest to the 'centre', taken as the intensity barycentre. This is the python
version of getroot.f of anaamika."""
import functions as func
root = None
npoint = len(xfn)
error = 0
if npoint == 0:
error = 1
elif yfn.max() * yfn.min() >= 0.0:
error = 1
minint = 0
minintold = 0
for i in range(1, npoint):
if yfn[i - 1] * yfn[i] < 0.0:
if minintold == 0: # so take nearest to centre
if abs(yfn[i - 1]) < abs(yfn[i]):
minint = i - 1
else:
minint = i
else:
dnew = func.dist_2pt([xco, xfn[i]], [xcen, ycen])
dold = func.dist_2pt([xco, xfn[minintold]], [xcen, ycen])
if dnew <= dold:
minint = i
else:
minint = minintold
minintold = minint
if minint < 1 or minint > npoint:
error = 1
if error != 1:
low = minint - min(2, minint) # -1)
up = minint + min(2, npoint - 1 - minint) # python array indexing rubbish
nfit = up - low + 1
xfit = xfn[low : low + nfit]
yfit = yfn[low : low + nfit]
sig = N.ones(nfit)
smask = N.zeros(nfit, dtype=bool)
xx = [i for i in range(low, low + nfit)]
[c, m], errors = func.fit_mask_1d(xfit, yfit, sig, smask, func.poly, do_err=False, order=1)
root = -c / m
if root < xfn[low] or root > xfn[up]:
error = 1
return root, error
def edit_vorogenlist(self, vorogenP, frac):
""" Edit primary voronoi generator list. Each tile has a tile centre and can
have more than one generator to be averaged. tile_list is a list of arrays, indexed
by the tile number and each array is an array of numbers in the ngen list which are
the generators in that tile. xtile, ytile and snrtile are arrays of length number_of_tiles
and have x,y,snr of each tile. Group together generators
if closer than a fraction of dist to third closest."""
xgen, ygen, snrgen = vorogenP
flag = N.zeros(len(xgen))
coord=N.array([xgen,ygen]).transpose()
tile_list = []
tile_coord = []; tile_snr = []
for i in range(len(xgen)):
dist = N.array(map(lambda t: func.dist_2pt(coord[i], t), coord))
indi = N.argsort(dist)
sortdist = dist[indi]
if sortdist[1] < frac * sortdist[2]: # first is the element itself
if flag[indi[1]] + flag[i] == 0: # not already deleted from other pair
tile_list.append([i, indi[1]])
tile_coord.append((coord[i]*snrgen[i]+coord[indi[1]]*snrgen[indi[1]])/(snrgen[i]+snrgen[indi[1]]))
tile_snr.append(snrgen[i]+snrgen[indi[1]])
flag[i] = 1
flag[indi[1]] = 1
else:
if len(dist) > 3:
if sortdist[1]+sortdist[2] < 2.0*frac*sortdist[3]: # for 3 close-by sources
in1=indi[1]
in2=indi[2]
if flag[in1]+flag[in2]+flag[i] == 0: # not already deleted from others
tile_list.append([i, in1, in2])
tile_coord.append((coord[i]*snrgen[i]+coord[in1]*snrgen[in1]+coord[in2]*snrgen[in2]) \
/(snrgen[i]+snrgen[in1]+snrgen[in2]))
tile_snr.append(snrgen[i]+snrgen[in1]+snrgen[in2])
flag[i] = 1
flag[in1] = 1
flag[in2] = 1
else:
tile_list.append([i])
tile_coord.append(coord[i])
tile_snr.append(snrgen[i])
# Assign any leftover generators
for i in range(len(xgen)):
if flag[i] == 0:
tile_list.append([i])
tile_coord.append(coord[i])
tile_snr.append(snrgen[i])
return tile_list, tile_coord, tile_snr
def edit_vorogenlist(self, vorogenP, frac):
""" Edit primary voronoi generator list. Each tile has a tile centre and can
have more than one generator to be averaged. tile_list is a list of arrays, indexed
by the tile number and each array is an array of numbers in the ngen list which are
the generators in that tile. xtile, ytile and snrtile are arrays of length number_of_tiles
and have x,y,snr of each tile. Group together generators
if closer than a fraction of dist to third closest."""
xgen, ygen, snrgen = vorogenP
flag = N.zeros(len(xgen))
coord=N.array([xgen,ygen]).transpose()
tile_list = []
tile_coord = []; tile_snr = []
for i in range(len(xgen)):
dist = N.array(map(lambda t: func.dist_2pt(coord[i], t), coord))
indi = N.argsort(dist)
sortdist = dist[indi]
if sortdist[1] < frac * sortdist[2]: # first is the element itself
if flag[indi[1]] + flag[i] == 0: # not already deleted from other pair
tile_list.append([i, indi[1]])
tile_coord.append((coord[i]*snrgen[i]+coord[indi[1]]*snrgen[indi[1]])/(snrgen[i]+snrgen[indi[1]]))
tile_snr.append(snrgen[i]+snrgen[indi[1]])
flag[i] = 1
flag[indi[1]] = 1
else:
if len(dist) > 3:
if sortdist[1]+sortdist[2] < 2.0*frac*sortdist[3]: # for 3 close-by sources
in1=indi[1]
in2=indi[2]
if flag[in1]+flag[in2]+flag[i] == 0: # not already deleted from others
tile_list.append([i, in1, in2])
tile_coord.append((coord[i]*snrgen[i]+coord[in1]*snrgen[in1]+coord[in2]*snrgen[in2]) \
/(snrgen[i]+snrgen[in1]+snrgen[in2]))
tile_snr.append(snrgen[i]+snrgen[in1]+snrgen[in2])
flag[i] = 1
flag[in1] = 1
flag[in2] = 1
else:
tile_list.append([i])
tile_coord.append(coord[i])
tile_snr.append(snrgen[i])
# Assign any leftover generators
for i in range(len(xgen)):
if flag[i] == 0:
tile_list.append([i])
tile_coord.append(coord[i])
tile_snr.append(snrgen[i])
return tile_list, tile_coord, tile_snr
def inigaus_nobeam(self, isl, thr, beam, img):
""" To get initial guesses when the source sizes are very different
from the beam, and can also be elongated. Mainly in the context of
a-trous transform images. Need to arrive at a good guess of the sizes
and hence need to partition the image around the maxima first. Tried the
IFT watershed algo but with markers, it segments the island only around
the minima and not the whole island. Cant find a good weighting scheme
for tesselation either. Hence will try this :
Calculate number of maxima. If one, then take moment as initial
guess. If more than one, then moment of whole island is one of the
guesses if mom1 is within n pixels of one of the maxima. Else dont take
whole island moment. Instead, find minima on lines connecting all maxima
and use geometric mean of all minima of a peak as the size of that peak.
"""
from math import sqrt
from const import fwsig
import scipy.ndimage as nd
import functions as func
im = isl.image-isl.islmean
if img.opts.ini_method == 'curvature':
im_pos = -1.0 * func.make_curvature_map(isl.image-isl.islmean)
thr_pos = 0.0
else:
im_pos = im
thr_pos = -1e9
mask = isl.mask_active
av = img.clipped_mean
inipeak, iniposn, im1 = func.get_maxima(im, mask, thr_pos, isl.shape, beam, im_pos=im_pos)
npeak = len(iniposn)
gaul = []
av, stdnew, maxv, maxp, minv, minp = func.arrstatmask(im, mask)
mom = func.momanalmask_gaus(isl.image-isl.islmean, isl.mask_active, 0, 1.0, True)
if npeak <= 1:
g = (float(maxv), int(round(mom[1])), int(round(mom[2])), mom[3]/fwsig, \
mom[4]/fwsig, mom[5])
gaul.append(g)
if npeak > 1: # markers start from 1=background, watershed starts from 1=background
watershed, markers = func.watershed(im, mask=isl.mask_active)
nshed = N.max(markers)-1 # excluding background
xm, ym = N.transpose([N.where(markers==i) for i in range(1,nshed+2)])[0]
coords = [c for c in N.transpose([xm,ym])[1:]]
alldists = [func.dist_2pt(c1, c2) for c1 in coords for c2 in coords if N.any(c1!=c2)] # has double
meandist = N.mean(alldists) # mean dist between all pairs of markers
compact = []; invmask = []
for ished in range(nshed):
shedmask = N.where(watershed==ished+2, False, True) + isl.mask_active # good unmasked pixels = 0
imm = nd.binary_dilation(~shedmask, N.ones((3,3), int))
xbad, ybad = N.where((imm==1)*(im>im[xm[ished+1], ym[ished+1]]))
imm[xbad, ybad] = 0
invmask.append(imm); x, y = N.where(imm); xcen, ycen = N.mean(x), N.mean(y) # good pixels are now = 1
dist = func.dist_2pt([xcen, ycen], [xm[ished+1], ym[ished+1]])
if dist < max(3.0, meandist/4.0):
compact.append(True) # if not compact, break source + diffuse
else:
compact.append(False)
if not N.all(compact):
avsize = []
ind = N.where(compact)[0]
for i in ind: avsize.append(N.sum(invmask[i]))
avsize = sqrt(N.mean(N.array(avsize)))
for i in range(len(compact)):
if not compact[i]: # make them all compact
newmask = N.zeros(imm.shape, bool)
newmask[max(0,xm[i+1]-avsize/2):min(im.shape[0],xm[i+1]+avsize/2), \
max(0,ym[i+1]-avsize/2):min(im.shape[1],ym[i+1]+avsize/2)] = True
invmask[i] = invmask[i]*newmask
resid = N.zeros(im.shape, dtype=N.float32) # approx fit all compact ones
for i in range(nshed):
mask1 = ~invmask[i]
size = sqrt(N.sum(invmask))/fwsig
xf, yf = coords[i][0], coords[i][1]
p_ini = [im[xf, yf], xf, yf, size, size, 0.0]
x, y = N.indices(im.shape)
p, success = func.fit_gaus2d(im*invmask[i], p_ini, x, y)
resid = resid + func.gaus_2d(p, x, y)
gaul.append(p)
resid = im - resid
if not N.all(compact): # just add one gaussian to fit whole unmasked island
maxv = N.max(resid) # assuming resid has only diffuse emission. can be false
x, y = N.where(~isl.mask_active); xcen = N.mean(x); ycen = N.mean(y)
invm = ~isl.mask_active
#bound = invm - nd.grey_erosion(invm, footprint = N.ones((3,3), int)) # better to use bound for ellipse fitting
mom = func.momanalmask_gaus(invm, N.zeros(invm.shape, dtype=N.int16), 0, 1.0, True)
g = (maxv, xcen, ycen, mom[3]/fwsig, mom[4]/fwsig, mom[5]-90.)
gaul.append(g)
coords.append([xcen, ycen])
return gaul
