def __call__(self, img):
mylog = mylogger.logging.getLogger("PyBDSM." + img.log + "Shapefit")
bar = statusbar.StatusBar(
'Decomposing islands into shapelets ...... : ', 0, img.nisl)
opts = img.opts
if img.opts.shapelet_do:
if opts.quiet == False:
bar.start()
# Set up multiproccessing. First create a simple copy of the Image
# object that contains the minimal data needed.
opts_dict = opts.to_dict()
img_simple = Image(opts_dict)
img_simple.pixel_beamarea = img.pixel_beamarea
img_simple.pixel_beam = img.pixel_beam
img_simple.thresh_pix = img.thresh_pix
img_simple.minpix_isl = img.minpix_isl
img_simple.clipped_mean = img.clipped_mean
img_simple.shape = img.ch0_arr.shape
# Now call the parallel mapping function. Returns a list of
# [beta, centre, nmax, basis, cf] for each island
shap_list = mp.parallel_map(
func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_island),
img.islands, itertools.repeat(img_simple),
itertools.repeat(opts)),
numcores=opts.ncores,
bar=bar)
for id, isl in enumerate(img.islands):
beta, centre, nmax, basis, cf = shap_list[id]
isl.shapelet_beta = beta
isl.shapelet_centre = centre
isl.shapelet_posn_sky = img.pix2sky(centre)
isl.shapelet_posn_skyE = [0.0, 0.0, 0.0]
isl.shapelet_nmax = nmax
isl.shapelet_basis = basis
isl.shapelet_cf = cf
img.completed_Ops.append('shapelets')
def __call__(self, img):
mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Shapefit")
bar = statusbar.StatusBar('Decomposing islands into shapelets ...... : ', 0, img.nisl)
opts = img.opts
if img.opts.shapelet_do:
if opts.quiet == False:
bar.start()
# Set up multiproccessing. First create a simple copy of the Image
# object that contains the minimal data needed.
opts_dict = opts.to_dict()
img_simple = Image(opts_dict)
img_simple.pixel_beamarea = img.pixel_beamarea
img_simple.pixel_beam = img.pixel_beam
img_simple.thresh_pix = img.thresh_pix
img_simple.minpix_isl = img.minpix_isl
img_simple.clipped_mean = img.clipped_mean
img_simple.shape = img.ch0_arr.shape
# Now call the parallel mapping function. Returns a list of
# [beta, centre, nmax, basis, cf] for each island
shap_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_island),
img.islands, itertools.repeat(img_simple),
itertools.repeat(opts)), numcores=opts.ncores,
bar=bar)
for id, isl in enumerate(img.islands):
beta, centre, nmax, basis, cf = shap_list[id]
isl.shapelet_beta=beta
isl.shapelet_centre=centre
isl.shapelet_posn_sky=img.pix2sky(centre)
isl.shapelet_posn_skyE=[0.0, 0.0, 0.0]
isl.shapelet_nmax=nmax
isl.shapelet_basis=basis
isl.shapelet_cf=cf
img.completed_Ops.append('shapelets')
def __call__(self, img):
if img.opts.psf_vary_do:
mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Psf_Vary")
mylogger.userinfo(mylog, '\nEstimating PSF variations')
opts = img.opts
dir = img.basedir + '/misc/'
plot = False # debug figures
image = img.ch0_arr
try:
from astropy.io import fits as pyfits
old_pyfits = False
except ImportError, err:
from distutils.version import StrictVersion
import pyfits
if StrictVersion(pyfits.__version__) < StrictVersion('2.2'):
old_pyfits = True
else:
old_pyfits = False
if old_pyfits:
mylog.warning('PyFITS version is too old: psf_vary module skipped')
return
over = 2
generators = opts.psf_generators; nsig = opts.psf_nsig; kappa2 = opts.psf_kappa2
snrtop = opts.psf_snrtop; snrbot = opts.psf_snrbot; snrcutstack = opts.psf_snrcutstack
gencode = opts.psf_gencode; primarygen = opts.psf_primarygen; itess_method = opts.psf_itess_method
tess_sc = opts.psf_tess_sc; tess_fuzzy= opts.psf_tess_fuzzy
bright_snr_cut = opts.psf_high_snr
s_only = opts.psf_stype_only
if opts.psf_snrcut < 5.0:
mylogger.userinfo(mylog, "Value of psf_snrcut too low; increasing to 5")
snrcut = 5.0
else:
snrcut = opts.psf_snrcut
img.psf_snrcut = snrcut
if opts.psf_high_snr != None:
if opts.psf_high_snr < 10.0:
mylogger.userinfo(mylog, "Value of psf_high_snr too low; increasing to 10")
high_snrcut = 10.0
else:
high_snrcut = opts.psf_high_snr
else:
high_snrcut = opts.psf_high_snr
img.psf_high_snr = high_snrcut
wtfns=['unity', 'roundness', 'log10', 'sqrtlog10']
if 0 <= itess_method < 4: tess_method=wtfns[itess_method]
else: tess_method='unity'
### now put all relevant gaussian parameters into a list
ngaus = img.ngaus
nsrc = img.nsrc
num = N.zeros(nsrc, dtype=N.int32)
peak = N.zeros(nsrc)
xc = N.zeros(nsrc)
yc = N.zeros(nsrc)
bmaj = N.zeros(nsrc)
bmin = N.zeros(nsrc)
bpa = N.zeros(nsrc)
code = N.array(['']*nsrc);
rms = N.zeros(nsrc)
src_id_list = []
for i, src in enumerate(img.sources):
src_max = 0.0
for gmax in src.gaussians:
# Take only brightest Gaussian per source
if gmax.peak_flux > src_max:
src_max = gmax.peak_flux
g = gmax
num[i] = i
peak[i] = g.peak_flux
xc[i] = g.centre_pix[0]
yc[i] = g.centre_pix[1]
bmaj[i] = g.size_pix[0]
bmin[i] = g.size_pix[1]
bpa[i] = g.size_pix[2]
code[i] = img.sources[g.source_id].code
rms[i] = img.islands[g.island_id].rms
gauls = (num, peak, xc, yc, bmaj, bmin, bpa, code, rms)
tr_gauls = self.trans_gaul(gauls)
# takes gaussians with code=S and snr > snrcut.
if s_only:
tr = [n for n in tr_gauls if n[1]/n[8]>snrcut and n[7] == 'S']
else:
tr = [n for n in tr_gauls if n[1]/n[8]>snrcut]
g_gauls = self.trans_gaul(tr)
# computes statistics of fitted sizes. Same as psfvary_fullstat.f in fBDSM.
bmaj_a, bmaj_r, bmaj_ca, bmaj_cr, ni = _cbdsm.bstat(bmaj, None, nsig)
bmin_a, bmin_r, bmin_ca, bmin_cr, ni = _cbdsm.bstat(bmin, None, nsig)
bpa_a, bpa_r, bpa_ca, bpa_cr, ni = _cbdsm.bstat(bpa, None, nsig)
# get subset of sources deemed to be unresolved. Same as size_ksclip_wenss.f in fBDSM.
flag_unresolved = self.get_unresolved(g_gauls, img.beam, nsig, kappa2, over, img.psf_high_snr, plot)
# see how much the SNR-weighted sizes of unresolved sources differ from the synthesized beam.
wtsize_beam_snr = self.av_psf(g_gauls, img.beam, flag_unresolved)
# filter out resolved sources
tr_gaul = self.trans_gaul(g_gauls)
tr = [n for i, n in enumerate(tr_gaul) if flag_unresolved[i]]
g_gauls = self.trans_gaul(tr)
mylogger.userinfo(mylog, 'Number of unresolved sources', str(len(g_gauls[0])))
# get a list of voronoi generators. vorogenS has values (and not None) if generators='field'.
vorogenP, vorogenS = self.get_voronoi_generators(g_gauls, generators, gencode, snrcut, snrtop, snrbot, snrcutstack)
mylogger.userinfo(mylog, 'Number of generators for PSF variation', str(len(vorogenP[0])))
if len(vorogenP[0]) < 3:
mylog.warning('Insufficient number of generators')
return
mylogger.userinfo(mylog, 'Tesselating image')
# group generators into tiles
tile_prop = self.edit_vorogenlist(vorogenP, frac=0.9)
# tesselate the image
volrank, vorowts = self.tesselate(vorogenP, vorogenS, tile_prop, tess_method, tess_sc, tess_fuzzy, \
generators, gencode, image.shape)
if opts.output_all:
func.write_image_to_file(img.use_io, img.imagename + '.volrank.fits', volrank, img, dir)
tile_list, tile_coord, tile_snr = tile_prop
ntile = len(tile_list)
bar = statusbar.StatusBar('Determining PSF variation ............... : ', 0, ntile)
mylogger.userinfo(mylog, 'Number of tiles for PSF variation', str(ntile))
# For each tile, calculate the weighted averaged psf image. Also for all the sources in the image.
cdelt = list(img.wcs_obj.acdelt[0:2])
factor=3.
psfimages, psfcoords, totpsfimage, psfratio, psfratio_aper = self.psf_in_tile(image, img.beam, g_gauls, \
cdelt, factor, snrcutstack, volrank, tile_prop, plot, img)
npsf = len(psfimages)
if opts.psf_use_shap:
# use totpsfimage to get beta, centre and nmax for shapelet decomposition. Use nmax=5 or 6
mask=N.zeros(totpsfimage.shape, dtype=bool)
(m1, m2, m3)=func.moment(totpsfimage, mask)
betainit=sqrt(m3[0]*m3[1])*2.0 * 1.4
tshape = totpsfimage.shape
cen = N.array(N.unravel_index(N.argmax(totpsfimage), tshape))+[1,1]
cen = tuple(cen)
nmax = 12
basis = 'cartesian'
betarange = [0.5,sqrt(betainit*max(tshape))]
beta, error = sh.shape_varybeta(totpsfimage, mask, basis, betainit, cen, nmax, betarange, plot)
if error == 1: print ' Unable to find minimum in beta'
# decompose all the psf images using the beta from above
nmax=12; psf_cf=[]
for i in range(npsf):
psfim = psfimages[i]
cf = sh.decompose_shapelets(psfim, mask, basis, beta, cen, nmax, mode='')
psf_cf.append(cf)
if img.opts.quiet == False:
bar.increment()
bar.stop()
# transpose the psf image list
xt, yt = N.transpose(tile_coord)
tr_psf_cf = N.transpose(N.array(psf_cf))
# interpolate the coefficients across the image. Ok, interpolate in scipy for
# irregular grids is crap. doesnt even pass through some of the points.
# for now, fit polynomial.
compress = 100.0
x, y = N.transpose(psfcoords)
if len(x) < 3:
mylog.warning('Insufficient number of tiles to do interpolation of PSF variation')
return
psf_coeff_interp, xgrid, ygrid = self.interp_shapcoefs(nmax, tr_psf_cf, psfcoords, image.shape, \
compress, plot)
psfshape = psfimages[0].shape
skip = 5
aa = self.create_psf_grid(psf_coeff_interp, image.shape, xgrid, ygrid, skip, nmax, psfshape, \
basis, beta, cen, totpsfimage, plot)
img.psf_images = aa
else:
if ntile < 4:
mylog.warning('Insufficient number of tiles to do interpolation of PSF variation')
return
else:
# Fit stacked PSFs with Gaussians and measure aperture fluxes
bm_pix = N.array([img.pixel_beam()[0]*fwsig, img.pixel_beam()[1]*fwsig, img.pixel_beam()[2]])
psf_maj = N.zeros(npsf)
psf_min = N.zeros(npsf)
psf_pa = N.zeros(npsf)
if img.opts.quiet == False:
bar.start()
for i in range(ntile):
psfim = psfimages[i]
mask = N.zeros(psfim.shape, dtype=bool)
x_ax, y_ax = N.indices(psfim.shape)
maxv = N.max(psfim)
p_ini = [maxv, (psfim.shape[0]-1)/2.0*1.1, (psfim.shape[1]-1)/2.0*1.1, bm_pix[0]/fwsig*1.3,
bm_pix[1]/fwsig*1.1, bm_pix[2]*2]
para, ierr = func.fit_gaus2d(psfim, p_ini, x_ax, y_ax, mask)
### first extent is major
if para[3] < para[4]:
para[3:5] = para[4:2:-1]
para[5] += 90
### clip position angle
para[5] = divmod(para[5], 180)[1]
psf_maj[i] = para[3]
psf_min[i] = para[4]
posang = para[5]
while posang >= 180.0:
posang -= 180.0
psf_pa[i] = posang
if img.opts.quiet == False:
bar.increment()
bar.stop()
# Interpolate Gaussian parameters
if img.aperture == None:
psf_maps = [psf_maj, psf_min, psf_pa, psfratio]
else:
psf_maps = [psf_maj, psf_min, psf_pa, psfratio, psfratio_aper]
nimgs = len(psf_maps)
bar = statusbar.StatusBar('Interpolating PSF images ................ : ', 0, nimgs)
if img.opts.quiet == False:
bar.start()
map_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.interp_prop),
psf_maps, itertools.repeat(psfcoords),
itertools.repeat(image.shape)), numcores=opts.ncores,
bar=bar)
if img.aperture == None:
psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int = map_list
else:
psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int, psf_ratio_aper_int = map_list
# Smooth if desired
if img.opts.psf_smooth != None:
sm_scale = img.opts.psf_smooth / img.pix2beam([1.0, 1.0, 0.0])[0] / 3600.0 # pixels
if img.opts.aperture == None:
psf_maps = [psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int]
else:
psf_maps = [psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int, psf_ratio_aper_int]
nimgs = len(psf_maps)
bar = statusbar.StatusBar('Smoothing PSF images .................... : ', 0, nimgs)
if img.opts.quiet == False:
bar.start()
map_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.blur_image),
psf_maps, itertools.repeat(sm_scale)), numcores=opts.ncores,
bar=bar)
if img.aperture == None:
psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int = map_list
else:
psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int, psf_ratio_aper_int = map_list
# Make sure all smoothed, interpolated images are ndarrays
psf_maj_int = N.array(psf_maj_int)
psf_min_int = N.array(psf_min_int)
psf_pa_int = N.array(psf_pa_int)
psf_ratio_int = N.array(psf_ratio_int)
if img.aperture == None:
psf_ratio_aper_int = N.zeros(psf_maj_int.shape, dtype=N.float32)
else:
psf_ratio_aper_int = N.array(psf_ratio_aper_int, dtype=N.float32)
# Blank with NaNs if needed
mask = img.mask_arr
if isinstance(mask, N.ndarray):
pix_masked = N.where(mask == True)
psf_maj_int[pix_masked] = N.nan
psf_min_int[pix_masked] = N.nan
psf_pa_int[pix_masked] = N.nan
psf_ratio_int[pix_masked] = N.nan
psf_ratio_aper_int[pix_masked] = N.nan
# Store interpolated images. The major and minor axis images are
# the sigma in units of arcsec, the PA image in units of degrees east of
# north, the ratio images in units of 1/beam.
img.psf_vary_maj_arr = psf_maj_int * img.pix2beam([1.0, 1.0, 0.0])[0] * 3600.0 # sigma in arcsec
img.psf_vary_min_arr = psf_min_int * img.pix2beam([1.0, 1.0, 0.0])[0] * 3600.0 # sigma in arcsec
img.psf_vary_pa_arr = psf_pa_int
img.psf_vary_ratio_arr = psf_ratio_int # in 1/beam
img.psf_vary_ratio_aper_arr = psf_ratio_aper_int # in 1/beam
if opts.output_all:
func.write_image_to_file(img.use_io, img.imagename + '.psf_vary_maj.fits', img.psf_vary_maj_arr*fwsig, img, dir)
func.write_image_to_file(img.use_io, img.imagename + '.psf_vary_min.fits', img.psf_vary_min_arr*fwsig, img, dir)
func.write_image_to_file(img.use_io, img.imagename + '.psf_vary_pa.fits', img.psf_vary_pa_arr, img, dir)
func.write_image_to_file(img.use_io, img.imagename + '.psf_vary_ratio.fits', img.psf_vary_ratio_arr, img, dir)
func.write_image_to_file(img.use_io, img.imagename + '.psf_vary_ratio_aper.fits', img.psf_vary_ratio_aper_arr, img, dir)
# Loop through source and Gaussian lists and deconvolve the sizes using appropriate beam
bar2 = statusbar.StatusBar('Correcting deconvolved source sizes ..... : ', 0, img.nsrc)
if img.opts.quiet == False:
bar2.start()
for src in img.sources:
src_pos = img.sky2pix(src.posn_sky_centroid)
src_pos_int = (int(src_pos[0]), int(src_pos[1]))
gaus_c = img.gaus2pix(src.size_sky, src.posn_sky_centroid)
gaus_bm = [psf_maj_int[src_pos_int]*fwsig, psf_min_int[src_pos_int]*fwsig, psf_pa_int[src_pos_int]*fwsig]
gaus_dc, err = func.deconv2(gaus_bm, gaus_c)
src.deconv_size_sky = img.pix2gaus(gaus_dc, src_pos)
src.deconv_size_skyE = [0.0, 0.0, 0.0]
for g in src.gaussians:
gaus_c = img.gaus2pix(g.size_sky, src.posn_sky_centroid)
gaus_dc, err = func.deconv2(gaus_bm, gaus_c)
g.deconv_size_sky = img.pix2gaus(gaus_dc, g.centre_pix)
g.deconv_size_skyE = [0.0, 0.0, 0.0]
if img.opts.quiet == False:
bar2.spin()
if img.opts.quiet == False:
bar2.increment()
bar2.stop()
img.completed_Ops.append('psf_vary')
def __call__(self, img):
from time import time
import functions as func
import itertools
mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Gausfit")
if len(img.islands) == 0:
img.gaussians = []
img.ngaus = 0
img.total_flux_gaus = 0.0
img.completed_Ops.append('gausfit')
return img
bar = statusbar.StatusBar('Fitting islands with Gaussians .......... : ',
0, img.nisl)
opts = img.opts
if opts.quiet == False and opts.verbose_fitting == False:
bar.start()
iter_ngmax = 10
min_maxsize = 50.0
maxsize = opts.splitisl_maxsize
min_peak_size = 30.0
peak_size = opts.peak_maxsize
if maxsize < min_maxsize:
maxsize = min_maxsize
opts.splitisl_maxsize = min_maxsize
if peak_size < min_peak_size:
peak_size = min_peak_size
opts.peak_maxsize = min_peak_size
# Set up multiproccessing. First create a simple copy of the Image
# object that contains the minimal data needed.
opts_dict = opts.to_dict()
img_simple = Image(opts_dict)
img_simple.pixel_beamarea = img.pixel_beamarea
img_simple.pixel_beam = img.pixel_beam
img_simple.thresh_pix = img.thresh_pix
img_simple.minpix_isl = img.minpix_isl
img_simple.clipped_mean = img.clipped_mean
img_simple.beam2pix = img.beam2pix
img_simple.beam = img.beam
# Next, define the weights to use when distributing islands among cores.
# The weight should scale with the processing time. At the moment
# we use the island area, but other parameters may be better.
weights = []
for isl in img.islands:
weights.append(isl.size_active)
# Now call the parallel mapping function. Returns a list of [gaul, fgaul]
# for each island.
gaus_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_island),
img.islands, itertools.repeat(img_simple),
itertools.repeat(opts)), numcores=opts.ncores,
bar=bar, weights=weights)
for isl in img.islands:
### now convert gaussians into Gaussian objects and store
idx = isl.island_id
gaul = gaus_list[idx][0]
fgaul = gaus_list[idx][1]
dgaul = []
gaul = [Gaussian(img, par, idx, gidx)
for (gidx, par) in enumerate(gaul)]
if len(gaul) == 0:
# No good Gaussians were fit. In this case, make a dummy
# Gaussian located at the island center so
# that the source may still be included in output catalogs.
# These dummy Gaussians all have an ID of -1. They do not
# appear in any of the source or island Gaussian lists except
# the island dgaul list.
if opts.src_ra_dec != None:
# Center the dummy Gaussian on the user-specified source position
posn_isl = (isl.shape[0]/2.0, isl.shape[1]/2.0)
posn_img = (isl.shape[0]/2.0 + isl.origin[0], isl.shape[1]/2.0 + isl.origin[1])
par = [isl.image[posn_isl], posn_img[0], posn_img[1], 0.0, 0.0, 0.0]
else:
# Center the dummy Gaussian on the maximum pixel
posn = N.unravel_index(N.argmax(isl.image*~isl.mask_active), isl.shape) + N.array(isl.origin)
par = [isl.max_value, posn[0], posn[1], 0.0, 0.0, 0.0]
dgaul = [Gaussian(img, par, idx, -1)]
gidx = 0
fgaul= [Gaussian(img, par, idx, gidx + gidx2 + 1, flag)
for (gidx2, (flag, par)) in enumerate(fgaul)]
isl.gaul = gaul
isl.fgaul= fgaul
isl.dgaul = dgaul
gaussian_list = [g for isl in img.islands for g in isl.gaul]
img.gaussians = gaussian_list
### put in the serial number of the gaussians for the whole image
n = 0
nn = 0
tot_flux = 0.0
if img.waveletimage:
# store the wavelet scale for each Gaussian
# (wavelet img's have a img.j attribute)
j = img.j
else:
j = 0
for isl in img.islands:
m = 0
for g in isl.gaul:
n += 1; m += 1
g.gaus_num = n - 1
tot_flux += g.total_flux
for dg in isl.dgaul:
nn -= 1
dg.gaus_num = nn
isl.ngaus = m
img.ngaus = n
img.total_flux_gaus = tot_flux
mylogger.userinfo(mylog, "Total number of Gaussians fit to image",
str(n))
if not img._pi and not img.waveletimage:
mylogger.userinfo(mylog, "Total flux density in model", '%.3f Jy' %
tot_flux)
# Check if model flux is very different from sum of flux in image
if img.ch0_sum_jy > 0 and not img._pi:
if img.total_flux_gaus/img.ch0_sum_jy < 0.5 or \
img.total_flux_gaus/img.ch0_sum_jy > 2.0:
mylog.warn('Total flux density in model is %0.2f times sum of pixels '\
'in input image. Large residuals may remain.' %
(img.total_flux_gaus/img.ch0_sum_jy,))
# Check if there are many Gaussians with deconvolved size of 0 in one
# axis but not in the other. Don't bother to do this for wavelet images.
fraction_1d = self.check_for_1d_gaussians(img)
if fraction_1d > 0.5 and img.beam != None and img.waveletimage == False:
mylog.warn('After deconvolution, more than 50% of Gaussians are '\
"1-D. Unless you're fitting an extended source, "\
"beam may be incorrect.")
img.completed_Ops.append('gausfit')
return img
def rms_mean_map(self, arr, mask=False, kappa=3, box=None, ncores=None):
"""Calculate map of the mean/rms values
Parameters:
arr: 2D array with data
mask: mask
kappa: clipping for calculating rms/mean within each box
box: box parameters (box_size, box_step)
Returns:
axes: list of 2 arrays with coordinates of boxes alongside each axis
mean_map: map of mean values
rms_map: map of rms values
Description:
This function calculates clipped mean and rms maps for the array.
The algorithm is a moving-window algorithm, where mean&rms are
calculated within a window of a size (box_size * box_size), and the
window is stepped withing the image by steps of box_steps.
Special care is taken for the borders of the image -- outer borders
(where box doesn't fit properly) are given one extra round with a box
applied to the border of the image. Additionally outer values are
extrapolated to cover whole image size, to simplify further processing.
See also routine 'remap_axes' for 'inverting' axes array
Example:
for an input image of 100x100 pixels calling rms_mean_map with default
box parameters (50, 25) will result in the following:
axes = [array([ 0. , 24.5, 49.5, 74.5, 99. ]),
array([ 0. , 24.5, 49.5, 74.5, 99. ])]
mean_map = <5x5 array>
rms_map = <5x5 array>
rms_map[1,1] is calculated for arr[0:50, 0:50]
rms_map[2,1] is calculated for arr[25:75, 0:50]
...etc...
rms_map[0,0] is extrapolated as .5*(rms_map[0,1] + rms_map[1,0])
rms_map[0,1] is extrapolated as rms_map[1,1]
"""
mylog = mylogger.logging.getLogger("PyBDSM.RmsMean")
if box is None:
box = (50, 25)
if box[0] < box[1]:
raise RuntimeError('Box size is less than step size.')
# Some math first: boxcount is number of boxes alongsize each axis,
# bounds is non-zero for axes which have extra pixels beyond last box
BS, SS = box
imgshape = N.array(arr.shape)
# If boxize is less than 10% of image, use simple extrapolation to
# derive the edges of the mean and rms maps; otherwise, use padded
# versions of arr and mask to derive the mean and rms maps
if float(BS)/float(imgshape[0]) < 0.1 and \
float(BS)/float(imgshape[1]) < 0.1:
use_extrapolation = True
else:
use_extrapolation = False
if use_extrapolation:
boxcount = 1 + (imgshape - BS) / SS
bounds = N.asarray((boxcount - 1) * SS + BS < imgshape, dtype=int)
mapshape = 2 + boxcount + bounds
else:
boxcount = 1 + imgshape / SS
bounds = N.asarray((boxcount - 1) * SS < imgshape, dtype=int)
mapshape = boxcount + bounds
pad_border_size = int(BS / 2.0)
new_shape = (arr.shape[0] + 2 * pad_border_size,
arr.shape[1] + 2 * pad_border_size)
arr_pad = self.pad_array(arr, new_shape)
if mask is None:
mask_pad = None
else:
mask_pad = self.pad_array(mask, new_shape)
# Make arrays for calculated data
mean_map = N.zeros(mapshape, dtype=N.float32)
rms_map = N.zeros(mapshape, dtype=N.float32)
axes = [N.zeros(len, dtype=N.float32) for len in mapshape]
# Step 1: internal area of the image
# Make a list of coordinates to send to process_mean_rms_maps()
coord_list = []
ind_list = []
for i in range(boxcount[0]):
for j in range(boxcount[1]):
if use_extrapolation:
coord_list.append((i + 1, j + 1))
else:
coord_list.append((i, j))
ind_list.append([i * SS, i * SS + BS, j * SS, j * SS + BS])
# Now call the parallel mapping function. Returns a list of [mean, rms]
# for each coordinate.
if use_extrapolation:
cm_cr_list = mp.parallel_map(
func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_mean_rms_maps),
ind_list, itertools.repeat(mask),
itertools.repeat(arr), itertools.repeat(kappa)),
numcores=ncores)
else:
cm_cr_list = mp.parallel_map(
func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_mean_rms_maps),
ind_list, itertools.repeat(mask_pad),
itertools.repeat(arr_pad),
itertools.repeat(kappa)),
numcores=ncores)
for i, co in enumerate(coord_list):
cm, cr = cm_cr_list[i]
mean_map[co] = cm
rms_map[co] = cr
# Check if all regions have too few unmasked pixels
if mask is not None and N.size(N.where(mean_map != N.inf)) == 0:
raise RuntimeError("No unmasked regions from which to determine "\
"mean and rms maps")
# Step 2: borders of the image
if bounds[0]:
coord_list = []
ind_list = []
for j in range(boxcount[1]):
if use_extrapolation:
coord_list.append((-2, j + 1))
ind_list.append([-BS, arr.shape[0], j * SS, j * SS + BS])
else:
coord_list.append((-1, j))
ind_list.append(
[-BS, arr_pad.shape[0], j * SS, j * SS + BS])
if use_extrapolation:
cm_cr_list = mp.parallel_map(
func.eval_func_tuple,
itertools.izip(
itertools.repeat(self.process_mean_rms_maps), ind_list,
itertools.repeat(mask), itertools.repeat(arr),
itertools.repeat(kappa)),
numcores=ncores)
else:
cm_cr_list = mp.parallel_map(
func.eval_func_tuple,
itertools.izip(
itertools.repeat(self.process_mean_rms_maps), ind_list,
itertools.repeat(mask_pad), itertools.repeat(arr_pad),
itertools.repeat(kappa)),
numcores=ncores)
for i, co in enumerate(coord_list):
cm, cr = cm_cr_list[i]
mean_map[co] = cm
rms_map[co] = cr
if bounds[1]:
coord_list = []
ind_list = []
for i in range(boxcount[0]):
if use_extrapolation:
coord_list.append((i + 1, -2))
ind_list.append([i * SS, i * SS + BS, -BS, arr.shape[1]])
else:
coord_list.append((i, -1))
ind_list.append(
[i * SS, i * SS + BS, -BS, arr_pad.shape[1]])
if use_extrapolation:
cm_cr_list = mp.parallel_map(
func.eval_func_tuple,
itertools.izip(
itertools.repeat(self.process_mean_rms_maps), ind_list,
itertools.repeat(mask), itertools.repeat(arr),
itertools.repeat(kappa)),
numcores=ncores)
else:
cm_cr_list = mp.parallel_map(
func.eval_func_tuple,
itertools.izip(
itertools.repeat(self.process_mean_rms_maps), ind_list,
itertools.repeat(mask_pad), itertools.repeat(arr_pad),
itertools.repeat(kappa)),
numcores=ncores)
for i, co in enumerate(coord_list):
cm, cr = cm_cr_list[i]
mean_map[co] = cm
rms_map[co] = cr
if bounds.all():
if use_extrapolation:
ind = [-BS, arr.shape[0], -BS, arr.shape[1]]
self.for_masked(mean_map, rms_map, mask, arr, ind, kappa,
[-2, -2])
else:
ind = [-BS, arr_pad.shape[0], -BS, arr_pad.shape[1]]
self.for_masked(mean_map, rms_map, mask_pad, arr_pad, ind,
kappa, [-1, -1])
# Step 3: correct(extrapolate) borders of the image
def correct_borders(map):
map[0, :] = map[1, :]
map[:, 0] = map[:, 1]
map[-1, :] = map[-2, :]
map[:, -1] = map[:, -2]
map[0, 0] = (map[1, 0] + map[0, 1]) / 2.
map[-1, 0] = (map[-2, 0] + map[-1, 1]) / 2.
map[0, -1] = (map[0, -2] + map[1, -1]) / 2.
map[-1, -1] = (map[-2, -1] + map[-1, -2]) / 2.
if use_extrapolation:
correct_borders(mean_map)
correct_borders(rms_map)
# Step 4: fill in coordinate axes
for i in range(2):
if use_extrapolation:
axes[i][1:boxcount[i] + 1] = (N.arange(boxcount[i]) * SS +
BS / 2. - .5)
if bounds[i]:
axes[i][-2] = imgshape[i] - BS / 2. - .5
else:
axes[i][0:boxcount[i]] = N.arange(boxcount[i]) * SS - .5
if bounds[i]:
axes[i][-2] = imgshape[i] - .5
axes[i][-1] = imgshape[i] - 1
# Step 5: fill in boxes with < 5 unmasked pixels (set to values of
# N.inf)
unmasked_boxes = N.where(mean_map != N.inf)
if N.size(unmasked_boxes, 1) < mapshape[0] * mapshape[1]:
mean_map = self.fill_masked_regions(mean_map)
rms_map = self.fill_masked_regions(rms_map)
return axes, mean_map, rms_map
def __call__(self, img):
if img.opts.psf_vary_do:
mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Psf_Vary")
mylogger.userinfo(mylog, '\nEstimating PSF variations')
opts = img.opts
dir = img.basedir + '/misc/'
plot = False # debug figures
image = img.ch0_arr
try:
from astropy.io import fits as pyfits
old_pyfits = False
except ImportError, err:
from distutils.version import StrictVersion
import pyfits
if StrictVersion(pyfits.__version__) < StrictVersion('2.2'):
old_pyfits = True
else:
old_pyfits = False
if old_pyfits:
mylog.warning('PyFITS version is too old: psf_vary module skipped')
return
if opts.psf_fwhm is not None:
# User has specified a constant PSF to use, so skip PSF fitting/etc.
psf_maj = opts.psf_fwhm[0] # FWHM in deg
psf_min = opts.psf_fwhm[1] # FWHM in deg
psf_pa = opts.psf_fwhm[2] # PA in deg
mylogger.userinfo(mylog, 'Using constant PSF (major, minor, pos angle)',
'(%.5e, %.5e, %s) degrees' % (psf_maj, psf_maj,
round(psf_pa, 1)))
else:
# Use did not specify a constant PSF to use, so estimate it
over = 2
generators = opts.psf_generators; nsig = opts.psf_nsig; kappa2 = opts.psf_kappa2
snrtop = opts.psf_snrtop; snrbot = opts.psf_snrbot; snrcutstack = opts.psf_snrcutstack
gencode = opts.psf_gencode; primarygen = opts.psf_primarygen; itess_method = opts.psf_itess_method
tess_sc = opts.psf_tess_sc; tess_fuzzy= opts.psf_tess_fuzzy
bright_snr_cut = opts.psf_high_snr
s_only = opts.psf_stype_only
if opts.psf_snrcut < 5.0:
mylogger.userinfo(mylog, "Value of psf_snrcut too low; increasing to 5")
snrcut = 5.0
else:
snrcut = opts.psf_snrcut
img.psf_snrcut = snrcut
if opts.psf_high_snr is not None:
if opts.psf_high_snr < 10.0:
mylogger.userinfo(mylog, "Value of psf_high_snr too low; increasing to 10")
high_snrcut = 10.0
else:
high_snrcut = opts.psf_high_snr
else:
high_snrcut = opts.psf_high_snr
img.psf_high_snr = high_snrcut
wtfns=['unity', 'roundness', 'log10', 'sqrtlog10']
if 0 <= itess_method < 4: tess_method=wtfns[itess_method]
else: tess_method='unity'
### now put all relevant gaussian parameters into a list
ngaus = img.ngaus
nsrc = img.nsrc
num = N.zeros(nsrc, dtype=N.int32)
peak = N.zeros(nsrc)
xc = N.zeros(nsrc)
yc = N.zeros(nsrc)
bmaj = N.zeros(nsrc)
bmin = N.zeros(nsrc)
bpa = N.zeros(nsrc)
code = N.array(['']*nsrc);
rms = N.zeros(nsrc)
src_id_list = []
for i, src in enumerate(img.sources):
src_max = 0.0
for gmax in src.gaussians:
# Take only brightest Gaussian per source
if gmax.peak_flux > src_max:
src_max = gmax.peak_flux
g = gmax
num[i] = i
peak[i] = g.peak_flux
xc[i] = g.centre_pix[0]
yc[i] = g.centre_pix[1]
bmaj[i] = g.size_pix[0]
bmin[i] = g.size_pix[1]
bpa[i] = g.size_pix[2]
code[i] = img.sources[g.source_id].code
rms[i] = img.islands[g.island_id].rms
gauls = (num, peak, xc, yc, bmaj, bmin, bpa, code, rms)
tr_gauls = self.trans_gaul(gauls)
# takes gaussians with code=S and snr > snrcut.
if s_only:
tr = [n for n in tr_gauls if n[1]/n[8]>snrcut and n[7] == 'S']
else:
tr = [n for n in tr_gauls if n[1]/n[8]>snrcut]
g_gauls = self.trans_gaul(tr)
# computes statistics of fitted sizes. Same as psfvary_fullstat.f in fBDSM.
bmaj_a, bmaj_r, bmaj_ca, bmaj_cr, ni = _cbdsm.bstat(bmaj, None, nsig)
bmin_a, bmin_r, bmin_ca, bmin_cr, ni = _cbdsm.bstat(bmin, None, nsig)
bpa_a, bpa_r, bpa_ca, bpa_cr, ni = _cbdsm.bstat(bpa, None, nsig)
# get subset of sources deemed to be unresolved. Same as size_ksclip_wenss.f in fBDSM.
flag_unresolved = self.get_unresolved(g_gauls, img.beam, nsig, kappa2, over, img.psf_high_snr, plot)
if len(flag_unresolved) == 0:
mylog.warning('Insufficient number of sources to determine PSF variation.\nTry changing the PSF options or specify a (constant) PSF with the "psf_fwhm" option')
return
# see how much the SNR-weighted sizes of unresolved sources differ from the synthesized beam.
wtsize_beam_snr = self.av_psf(g_gauls, img.beam, flag_unresolved)
# filter out resolved sources
tr_gaul = self.trans_gaul(g_gauls)
tr = [n for i, n in enumerate(tr_gaul) if flag_unresolved[i]]
g_gauls = self.trans_gaul(tr)
mylogger.userinfo(mylog, 'Number of unresolved sources', str(len(g_gauls[0])))
# get a list of voronoi generators. vorogenS has values (and not None) if generators='field'.
vorogenP, vorogenS = self.get_voronoi_generators(g_gauls, generators, gencode, snrcut, snrtop, snrbot, snrcutstack)
mylogger.userinfo(mylog, 'Number of generators for PSF variation', str(len(vorogenP[0])))
if len(vorogenP[0]) < 3:
mylog.warning('Insufficient number of generators')
return
mylogger.userinfo(mylog, 'Tesselating image')
# group generators into tiles
tile_prop = self.edit_vorogenlist(vorogenP, frac=0.9)
# tesselate the image
volrank, vorowts = self.tesselate(vorogenP, vorogenS, tile_prop, tess_method, tess_sc, tess_fuzzy, \
generators, gencode, image.shape)
if opts.output_all:
func.write_image_to_file(img.use_io, img.imagename + '.volrank.fits', volrank, img, dir)
tile_list, tile_coord, tile_snr = tile_prop
ntile = len(tile_list)
bar = statusbar.StatusBar('Determining PSF variation ............... : ', 0, ntile)
mylogger.userinfo(mylog, 'Number of tiles for PSF variation', str(ntile))
# For each tile, calculate the weighted averaged psf image. Also for all the sources in the image.
cdelt = list(img.wcs_obj.acdelt[0:2])
factor=3.
psfimages, psfcoords, totpsfimage, psfratio, psfratio_aper = self.psf_in_tile(image, img.beam, g_gauls, \
cdelt, factor, snrcutstack, volrank, tile_prop, plot, img)
npsf = len(psfimages)
if opts.psf_use_shap:
if opts.psf_fwhm is None:
# use totpsfimage to get beta, centre and nmax for shapelet decomposition. Use nmax=5 or 6
mask=N.zeros(totpsfimage.shape, dtype=bool)
(m1, m2, m3)=func.moment(totpsfimage, mask)
betainit=sqrt(m3[0]*m3[1])*2.0 * 1.4
tshape = totpsfimage.shape
cen = N.array(N.unravel_index(N.argmax(totpsfimage), tshape))+[1,1]
cen = tuple(cen)
nmax = 12
basis = 'cartesian'
betarange = [0.5,sqrt(betainit*max(tshape))]
beta, error = sh.shape_varybeta(totpsfimage, mask, basis, betainit, cen, nmax, betarange, plot)
if error == 1: print ' Unable to find minimum in beta'
# decompose all the psf images using the beta from above
nmax=12; psf_cf=[]
for i in range(npsf):
psfim = psfimages[i]
cf = sh.decompose_shapelets(psfim, mask, basis, beta, cen, nmax, mode='')
psf_cf.append(cf)
if img.opts.quiet == False:
bar.increment()
bar.stop()
# transpose the psf image list
xt, yt = N.transpose(tile_coord)
tr_psf_cf = N.transpose(N.array(psf_cf))
# interpolate the coefficients across the image. Ok, interpolate in scipy for
# irregular grids is crap. doesnt even pass through some of the points.
# for now, fit polynomial.
compress = 100.0
x, y = N.transpose(psfcoords)
if len(x) < 3:
mylog.warning('Insufficient number of tiles to do interpolation of PSF variation')
return
psf_coeff_interp, xgrid, ygrid = self.interp_shapcoefs(nmax, tr_psf_cf, psfcoords, image.shape, \
compress, plot)
psfshape = psfimages[0].shape
skip = 5
aa = self.create_psf_grid(psf_coeff_interp, image.shape, xgrid, ygrid, skip, nmax, psfshape, \
basis, beta, cen, totpsfimage, plot)
img.psf_images = aa
else:
if opts.psf_fwhm is None:
if ntile < 4:
mylog.warning('Insufficient number of tiles to do interpolation of PSF variation')
return
else:
# Fit stacked PSFs with Gaussians and measure aperture fluxes
bm_pix = N.array([img.pixel_beam()[0]*fwsig, img.pixel_beam()[1]*fwsig, img.pixel_beam()[2]])
psf_maj = N.zeros(npsf)
psf_min = N.zeros(npsf)
psf_pa = N.zeros(npsf)
if img.opts.quiet == False:
bar.start()
for i in range(ntile):
psfim = psfimages[i]
mask = N.zeros(psfim.shape, dtype=bool)
x_ax, y_ax = N.indices(psfim.shape)
maxv = N.max(psfim)
p_ini = [maxv, (psfim.shape[0]-1)/2.0*1.1, (psfim.shape[1]-1)/2.0*1.1, bm_pix[0]/fwsig*1.3,
bm_pix[1]/fwsig*1.1, bm_pix[2]*2]
para, ierr = func.fit_gaus2d(psfim, p_ini, x_ax, y_ax, mask)
### first extent is major
if para[3] < para[4]:
para[3:5] = para[4:2:-1]
para[5] += 90
### clip position angle
para[5] = divmod(para[5], 180)[1]
psf_maj[i] = para[3]
psf_min[i] = para[4]
posang = para[5]
while posang >= 180.0:
posang -= 180.0
psf_pa[i] = posang
if img.opts.quiet == False:
bar.increment()
bar.stop()
# Interpolate Gaussian parameters
if img.aperture is None:
psf_maps = [psf_maj, psf_min, psf_pa, psfratio]
else:
psf_maps = [psf_maj, psf_min, psf_pa, psfratio, psfratio_aper]
nimgs = len(psf_maps)
bar = statusbar.StatusBar('Interpolating PSF images ................ : ', 0, nimgs)
if img.opts.quiet == False:
bar.start()
map_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.interp_prop),
psf_maps, itertools.repeat(psfcoords),
itertools.repeat(image.shape)), numcores=opts.ncores,
bar=bar)
if img.aperture is None:
psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int = map_list
else:
psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int, psf_ratio_aper_int = map_list
# Smooth if desired
if img.opts.psf_smooth is not None:
sm_scale = img.opts.psf_smooth / img.pix2beam([1.0, 1.0, 0.0])[0] / 3600.0 # pixels
if img.opts.aperture is None:
psf_maps = [psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int]
else:
psf_maps = [psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int, psf_ratio_aper_int]
nimgs = len(psf_maps)
bar = statusbar.StatusBar('Smoothing PSF images .................... : ', 0, nimgs)
if img.opts.quiet == False:
bar.start()
map_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.blur_image),
psf_maps, itertools.repeat(sm_scale)), numcores=opts.ncores,
bar=bar)
if img.aperture is None:
psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int = map_list
else:
psf_maj_int, psf_min_int, psf_pa_int, psf_ratio_int, psf_ratio_aper_int = map_list
# Make sure all smoothed, interpolated images are ndarrays
psf_maj_int = N.array(psf_maj_int)
psf_min_int = N.array(psf_min_int)
psf_pa_int = N.array(psf_pa_int)
psf_ratio_int = N.array(psf_ratio_int)
if img.aperture is None:
psf_ratio_aper_int = N.zeros(psf_maj_int.shape, dtype=N.float32)
else:
psf_ratio_aper_int = N.array(psf_ratio_aper_int, dtype=N.float32)
# Blank with NaNs if needed
mask = img.mask_arr
if isinstance(mask, N.ndarray):
pix_masked = N.where(mask == True)
psf_maj_int[pix_masked] = N.nan
psf_min_int[pix_masked] = N.nan
psf_pa_int[pix_masked] = N.nan
psf_ratio_int[pix_masked] = N.nan
psf_ratio_aper_int[pix_masked] = N.nan
# Store interpolated images. The major and minor axis images are
# the sigma in units of arcsec, the PA image in units of degrees east of
# north, the ratio images in units of 1/beam.
img.psf_vary_maj_arr = psf_maj_int * img.pix2beam([1.0, 1.0, 0.0])[0] * 3600.0 # sigma in arcsec
img.psf_vary_min_arr = psf_min_int * img.pix2beam([1.0, 1.0, 0.0])[0] * 3600.0 # sigma in arcsec
img.psf_vary_pa_arr = psf_pa_int
img.psf_vary_ratio_arr = psf_ratio_int # in 1/beam
img.psf_vary_ratio_aper_arr = psf_ratio_aper_int # in 1/beam
if opts.output_all:
func.write_image_to_file(img.use_io, img.imagename + '.psf_vary_maj.fits', img.psf_vary_maj_arr*fwsig, img, dir)
func.write_image_to_file(img.use_io, img.imagename + '.psf_vary_min.fits', img.psf_vary_min_arr*fwsig, img, dir)
func.write_image_to_file(img.use_io, img.imagename + '.psf_vary_pa.fits', img.psf_vary_pa_arr, img, dir)
func.write_image_to_file(img.use_io, img.imagename + '.psf_vary_ratio.fits', img.psf_vary_ratio_arr, img, dir)
func.write_image_to_file(img.use_io, img.imagename + '.psf_vary_ratio_aper.fits', img.psf_vary_ratio_aper_arr, img, dir)
# Loop through source and Gaussian lists and deconvolve the sizes using appropriate beam
bar2 = statusbar.StatusBar('Correcting deconvolved source sizes ..... : ', 0, img.nsrc)
if img.opts.quiet == False:
bar2.start()
for src in img.sources:
src_pos = img.sky2pix(src.posn_sky_centroid)
src_pos_int = (int(src_pos[0]), int(src_pos[1]))
gaus_c = img.gaus2pix(src.size_sky, src.posn_sky_centroid)
if opts.psf_fwhm is None:
gaus_bm = [psf_maj_int[src_pos_int]*fwsig, psf_min_int[src_pos_int]*fwsig, psf_pa_int[src_pos_int]]
else:
# Use user-specified constant PSF instead
gaus_bm = img.beam2pix(opts.psf_fwhm)
gaus_dc, err = func.deconv2(gaus_bm, gaus_c)
src.deconv_size_sky = img.pix2gaus(gaus_dc, src_pos)
src.deconv_size_skyE = [0.0, 0.0, 0.0]
for g in src.gaussians:
gaus_c = img.gaus2pix(g.size_sky, src.posn_sky_centroid)
gaus_dc, err = func.deconv2(gaus_bm, gaus_c)
g.deconv_size_sky = img.pix2gaus(gaus_dc, g.centre_pix)
g.deconv_size_skyE = [0.0, 0.0, 0.0]
if img.opts.quiet == False:
bar2.spin()
if img.opts.quiet == False:
bar2.increment()
bar2.stop()
img.completed_Ops.append('psf_vary')
def rms_mean_map(self, arr, mask=False, kappa=3, box=None, ncores=None):
"""Calculate map of the mean/rms values
Parameters:
arr: 2D array with data
mask: mask
kappa: clipping for calculating rms/mean within each box
box: box parameters (box_size, box_step)
Returns:
axes: list of 2 arrays with coordinates of boxes alongside each axis
mean_map: map of mean values
rms_map: map of rms values
Description:
This function calculates clipped mean and rms maps for the array.
The algorithm is a moving-window algorithm, where mean&rms are
calculated within a window of a size (box_size * box_size), and the
window is stepped withing the image by steps of box_steps.
Special care is taken for the borders of the image -- outer borders
(where box doesn't fit properly) are given one extra round with a box
applied to the border of the image. Additionally outer values are
extrapolated to cover whole image size, to simplify further processing.
See also routine 'remap_axes' for 'inverting' axes array
Example:
for an input image of 100x100 pixels calling rms_mean_map with default
box parameters (50, 25) will result in the following:
axes = [array([ 0. , 24.5, 49.5, 74.5, 99. ]),
array([ 0. , 24.5, 49.5, 74.5, 99. ])]
mean_map = <5x5 array>
rms_map = <5x5 array>
rms_map[1,1] is calculated for arr[0:50, 0:50]
rms_map[2,1] is calculated for arr[25:75, 0:50]
...etc...
rms_map[0,0] is extrapolated as .5*(rms_map[0,1] + rms_map[1,0])
rms_map[0,1] is extrapolated as rms_map[1,1]
"""
mylog = mylogger.logging.getLogger("PyBDSM.RmsMean")
if box is None:
box = (50, 25)
if box[0] < box[1]:
raise RuntimeError('Box size is less than step size.')
# Some math first: boxcount is number of boxes alongsize each axis,
# bounds is non-zero for axes which have extra pixels beyond last box
BS, SS = box
imgshape = N.array(arr.shape)
# If boxize is less than 10% of image, use simple extrapolation to
# derive the edges of the mean and rms maps; otherwise, use padded
# versions of arr and mask to derive the mean and rms maps
if float(BS)/float(imgshape[0]) < 0.1 and \
float(BS)/float(imgshape[1]) < 0.1:
use_extrapolation = True
else:
use_extrapolation = False
if use_extrapolation:
boxcount = 1 + (imgshape - BS)/SS
bounds = N.asarray((boxcount-1)*SS + BS < imgshape, dtype=int)
mapshape = 2 + boxcount + bounds
else:
boxcount = 1 + imgshape/SS
bounds = N.asarray((boxcount-1)*SS < imgshape, dtype=int)
mapshape = boxcount + bounds
pad_border_size = int(BS/2.0)
new_shape = (arr.shape[0] + 2*pad_border_size, arr.shape[1]
+ 2*pad_border_size)
arr_pad = self.pad_array(arr, new_shape)
if mask == None:
mask_pad = None
else:
mask_pad = self.pad_array(mask, new_shape)
# Make arrays for calculated data
mean_map = N.zeros(mapshape, dtype=N.float32)
rms_map = N.zeros(mapshape, dtype=N.float32)
axes = [N.zeros(len, dtype=N.float32) for len in mapshape]
# Step 1: internal area of the image
# Make a list of coordinates to send to process_mean_rms_maps()
coord_list = []
ind_list = []
for i in range(boxcount[0]):
for j in range(boxcount[1]):
if use_extrapolation:
coord_list.append((i+1, j+1))
else:
coord_list.append((i, j))
ind_list.append([i*SS, i*SS+BS, j*SS, j*SS+BS])
# Now call the parallel mapping function. Returns a list of [mean, rms]
# for each coordinate.
if use_extrapolation:
cm_cr_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_mean_rms_maps),
ind_list, itertools.repeat(mask), itertools.repeat(arr),
itertools.repeat(kappa)), numcores=ncores)
else:
cm_cr_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_mean_rms_maps),
ind_list, itertools.repeat(mask_pad), itertools.repeat(arr_pad),
itertools.repeat(kappa)), numcores=ncores)
for i, co in enumerate(coord_list):
cm, cr = cm_cr_list[i]
mean_map[co] = cm
rms_map[co] = cr
# Check if all regions have too few unmasked pixels
if mask != None and N.size(N.where(mean_map != N.inf)) == 0:
raise RuntimeError("No unmasked regions from which to determine "\
"mean and rms maps")
# Step 2: borders of the image
if bounds[0]:
coord_list = []
ind_list = []
for j in range(boxcount[1]):
if use_extrapolation:
coord_list.append((-2, j+1))
ind_list.append([-BS, arr.shape[0], j*SS,j*SS+BS])
else:
coord_list.append((-1, j))
ind_list.append([-BS, arr_pad.shape[0], j*SS,j*SS+BS])
if use_extrapolation:
cm_cr_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_mean_rms_maps),
ind_list, itertools.repeat(mask), itertools.repeat(arr),
itertools.repeat(kappa)), numcores=ncores)
else:
cm_cr_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_mean_rms_maps),
ind_list, itertools.repeat(mask_pad), itertools.repeat(arr_pad),
itertools.repeat(kappa)), numcores=ncores)
for i, co in enumerate(coord_list):
cm, cr = cm_cr_list[i]
mean_map[co] = cm
rms_map[co] = cr
if bounds[1]:
coord_list = []
ind_list = []
for i in range(boxcount[0]):
if use_extrapolation:
coord_list.append((i+1, -2))
ind_list.append([i*SS,i*SS+BS, -BS,arr.shape[1]])
else:
coord_list.append((i, -1))
ind_list.append([i*SS,i*SS+BS, -BS,arr_pad.shape[1]])
if use_extrapolation:
cm_cr_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_mean_rms_maps),
ind_list, itertools.repeat(mask), itertools.repeat(arr),
itertools.repeat(kappa)), numcores=ncores)
else:
cm_cr_list = mp.parallel_map(func.eval_func_tuple,
itertools.izip(itertools.repeat(self.process_mean_rms_maps),
ind_list, itertools.repeat(mask_pad), itertools.repeat(arr_pad),
itertools.repeat(kappa)), numcores=ncores)
for i, co in enumerate(coord_list):
cm, cr = cm_cr_list[i]
mean_map[co] = cm
rms_map[co] = cr
if bounds.all():
if use_extrapolation:
ind = [-BS,arr.shape[0], -BS,arr.shape[1]]
self.for_masked(mean_map, rms_map, mask, arr, ind,
kappa, [-2, -2])
else:
ind = [-BS,arr_pad.shape[0], -BS,arr_pad.shape[1]]
self.for_masked(mean_map, rms_map, mask_pad, arr_pad, ind,
kappa, [-1, -1])
# Step 3: correct(extrapolate) borders of the image
def correct_borders(map):
map[0, :] = map[1, :]
map[:, 0] = map[:, 1]
map[-1, :] = map[-2, :]
map[:, -1] = map[:, -2]
map[0,0] = (map[1,0] + map[0, 1])/2.
map[-1,0] = (map[-2, 0] + map[-1, 1])/2.
map[0, -1] = (map[0, -2] + map[1, -1])/2.
map[-1,-1] = (map[-2, -1] + map[-1, -2])/2.
if use_extrapolation:
correct_borders(mean_map)
correct_borders(rms_map)
# Step 4: fill in coordinate axes
for i in range(2):
if use_extrapolation:
axes[i][1:boxcount[i]+1] = (N.arange(boxcount[i])*SS
+ BS/2. - .5)
if bounds[i]:
axes[i][-2] = imgshape[i] - BS/2. - .5
else:
axes[i][0:boxcount[i]] = N.arange(boxcount[i])*SS - .5
if bounds[i]:
axes[i][-2] = imgshape[i] - .5
axes[i][-1] = imgshape[i] - 1
# Step 5: fill in boxes with < 5 unmasked pixels (set to values of
# N.inf)
unmasked_boxes = N.where(mean_map != N.inf)
if N.size(unmasked_boxes,1) < mapshape[0]*mapshape[1]:
mean_map = self.fill_masked_regions(mean_map)
rms_map = self.fill_masked_regions(rms_map)
return axes, mean_map, rms_map