def bigger_wsdl(self, band, compare=None):
""" Want to sample on a grid that is comparable in size (or
smaller than) 10% of the psf to ensure we get a reasonable
sampling of the grid. """
if compare is None:
r10 = band.psf.inverse_integral_on_axis(0.10)
compare = r10
self.factor = int(np.ceil(self.pixelsize / compare))
if self.factor == 1:
return self.wsdl
else:
# hold onto this thing since it is needed by downsample_model
if not hasattr(self.size, '__iter__'):
self.fine_skyimage = SkyImage(
self.center, '',
float(self.pixelsize) / self.factor, self.size, 1,
self.proj, self.galactic, False)
else:
self.fine_skyimage = SkyImage(
self.center, '',
float(self.pixelsize) / self.factor, float(self.size[0]),
1, self.proj, self.galactic, False, float(self.size[1]))
wsdl = self.fine_skyimage.get_wsdl()
return wsdl
def load_skyspect(fn = r'T:\data\galprop\ring_21month_P6v11.fits',
# r'D:\fermi\data\galprop\gll_iem_v02.fit',
nside=192,
show_kw = dict(fun=np.log10, cmap='hot'),
):
"""
load a galactic diffuse distribution.
Save the HEALpix respresentation at an energy (1 GeV default)
fn : string
filename for the FITS representaion of a SKySpectrum
nside: int
HEALpix nside to use for represenation -- note that 192 is 12*16, about 0.25 deg
show_kw : dict
fun: weighting function, cmap, vmin, vmax
"""
t = SkyImage(fn)
galname = os.path.split(fn)[-1]
print '%s: nx, ny, layers: %d %d %d' %(galname, t.naxis1(), t.naxis2(), t.layers())
hpdir = Band(nside).dir
dmap = map(lambda i:t(hpdir(i)), xrange(12*nside**2))
tdm=DisplayMap(dmap)
tdm.fill_ait(fignum=12, source_kw=dict(edgecolor='w',), show_kw=show_kw )
plt.title(galname+' (1 GeV)')
sfn = galname.split('.')[0]+'.png'
plt.savefig(galname.split('.')[0]+'.png', bbox_inches='tight', pad_inches=0)
print 'saved figure to %s' % sfn
return tdm
def __init__(
self,
name,
filename,
nside=512,
):
self.skyimage = SkyImage(filename)
super(HPfitscube, self).__init__(name, self.skyimage, nside)
class HPfitscube(HPskyfun):
""" generate from a FITS cube """
def __init__(self, name, filename, nside=512,):
self.skyimage=SkyImage(filename)
super(HPfitscube,self).__init__(name, self.skyimage, nside)
def set_layer(self,n):
# use 1-based indexing for layer umber
return self.skyimage.setLayer(n-1)+1
def layers(self): return self.skyimage.layers()
def __init__(self, roi, **kwargs):
""" Note, unlike ZEA, can support non-square images. To specify a nonsquare
image, set the size parameter to a lenght two tuple:
size=(10,5) # dx=10 degrees, dy=5 degrees.
"""
keyword_options.process(self, kwargs)
if self.size < self.pixelsize:
raise Exception("Can only create images with >=1 pixel in them.")
self.roi = roi
self.selected_bands = tuple(self.roi.bands if self.conv_type < 0 else \
[ band for band in self.roi.bands if band.ct == self.conv_type ])
# by default, use get energy range and image center from roi.
if self.center is None: self.center = self.roi.roi_dir
# set up, then create a SkyImage object to perform the projection
# to a grid and manage an image
if not isinstance(self.size, collections.Iterable):
# make sure size and pixelsize are commensurate (helpful for
# various downsampling code later).
self.size = int(self.size / self.pixelsize + 0.01) * self.pixelsize
self.skyimage = SkyImage(self.center, '', self.pixelsize,
self.size, 1, self.proj, self.galactic,
False)
else:
self.skyimage = SkyImage(self.center, '', self.pixelsize,
float(self.size[0]), 1, self.proj,
self.galactic, False, float(self.size[1]))
self.fill()
self.nx, self.ny = self.skyimage.naxis1(), self.skyimage.naxis2()
self.image = ROIImage.skyimage2numpy(self.skyimage)
def __init__(self, filename):
t = os.path.split(os.path.splitext(filename)[0])[-1].split('_')
self.sourcename = ' '.join(t[:-1]).replace('p', '+')
self.df = df = SkyImage(filename)
wcs = df.projector()
self.tsmap = np.array(df.image())
nx, ny = df.naxis1(), df.naxis2()
assert nx == ny, 'Array not square?'
vals = np.exp(-0.5 * self.tsmap**2) # convert to likelihood from TS
norm = 1. / sum(vals)
self.peak_fract = norm * vals.max()
center, variance = self.moments_analysis(vals)
ra, dec = wcs.pix2sph(center[1], center[0])
self.peak = SkyDir(ra, dec)
self.scale = wcs.pix2sph(center[0], center[1] + 1)[1] - dec
self.size = nx * self.scale
self.variance = self.scale**2 * variance
rac, decc = wcs.pix2sph(nx / 2, ny / 2)
self.offset = np.degrees(self.peak.difference(SkyDir(rac, decc)))
Author: Joshua Lande <*****@*****.**>
"""
from shutil import copy
from os.path import expandvars
from skymaps import SkyImage
from simulate import get_catalog, get_spatial
# First, load 2FGL w44
catalog=get_catalog()
w44=catalog.get_source('W44')
w44_spatial_map = w44.spatial_model
w44_file=expandvars(w44_spatial_map.file)
# Define a new analytic shape
w44_ring = get_spatial('EllipticalRing')
# Create a new spatial map with same binning as 2FGL tempalte, but filled with new analytic shape
new_template='pointlike_ring_template.fits'
copy(w44_file,new_template)
x=SkyImage(new_template)
x.fill(w44_ring.get_PySkyFunction())
x.save()
print 'original',w44_file
print 'new',new_template
class ROIImage(object):
""" This object is suitable for creating a SkyImage object
and filling it with some physically meaningful
quantity gotten from an ROIAnalysis object.
The acutal work is done by subclasses. """
defaults = (
('size', 2, 'size of image in degrees'),
('pixelsize', 0.1, 'size, in degrees, of pixels'),
('galactic', False, 'galactic or equatorial coordinates'),
('proj', 'ZEA', 'projection name: can change if desired'),
('center', None, 'Center of image. If None, use roi center.'),
('conv_type', -1, 'Conversion type'),
)
@keyword_options.decorate(defaults)
def __init__(self, roi, **kwargs):
""" Note, unlike ZEA, can support non-square images. To specify a nonsquare
image, set the size parameter to a lenght two tuple:
size=(10,5) # dx=10 degrees, dy=5 degrees.
"""
keyword_options.process(self, kwargs)
if self.size < self.pixelsize:
raise Exception("Can only create images with >=1 pixel in them.")
self.roi = roi
self.selected_bands = tuple(self.roi.bands if self.conv_type < 0 else \
[ band for band in self.roi.bands if band.ct == self.conv_type ])
# by default, use get energy range and image center from roi.
if self.center is None: self.center = self.roi.roi_dir
# set up, then create a SkyImage object to perform the projection
# to a grid and manage an image
if not isinstance(self.size, collections.Iterable):
# make sure size and pixelsize are commensurate (helpful for
# various downsampling code later).
self.size = int(self.size / self.pixelsize + 0.01) * self.pixelsize
self.skyimage = SkyImage(self.center, '', self.pixelsize,
self.size, 1, self.proj, self.galactic,
False)
else:
self.skyimage = SkyImage(self.center, '', self.pixelsize,
float(self.size[0]), 1, self.proj,
self.galactic, False, float(self.size[1]))
self.fill()
self.nx, self.ny = self.skyimage.naxis1(), self.skyimage.naxis2()
self.image = ROIImage.skyimage2numpy(self.skyimage)
@staticmethod
def skyimage2numpy(skyimage):
nx, ny = skyimage.naxis1(), skyimage.naxis2()
image = np.array(skyimage.image()).reshape((ny, nx))
return image
@abstractmethod
def fill(self):
pass
def get_ZEA(self, axes=None, nticks=None):
""" axes and nticks can be created by this object's constructor, but are
more logically specified here. If they are not specified, get values from
initial object creation. """
# get out of the object all parameters which should be passed to ZEA.
if hasattr(self.size, '__iter__'):
raise Exception("Can only create ZEA object for square objects.")
zea_dict = dict((d[0],self.__dict__[d[0]]) for d in ZEA.defaults if hasattr(d,'__iter__') and \
hasattr(self,d[0]))
if axes is not None: zea_dict['axes'] = axes
if nticks is not None: zea_dict['nticks'] = nticks
from uw.utilities.image import ZEA
zea = ZEA(self.center, **zea_dict)
zea.skyimage = self.skyimage
# recalculate, in case the sky image has changed
zea.image = ROIImage.skyimage2numpy(self.skyimage)
# The old one gets removed by python's garbage collector (when zea.skyimage is replaced).
zea.projector = zea.skyimage.projector()
zea.vmin, zea.vmax = zea.skyimage.minimum(), zea.skyimage.maximum()
return zea
def get_pyfits(self):
""" Create and return a pyfits object that corresponds to the ROIImage object.
The fits file created is supposed to be consistent with the internal
representation that SkyImage/SkyProj uses. """
if self.galactic:
ctype1 = "GLON-%s" % self.proj
ctype2 = "GLAT-%s" % self.proj
# for some reason, SkyDir(0,0,SkyDir.GALACTIC).l() = 360
crval1, crval2 = self.center.l() % 360, self.center.b()
else:
ctype1 = "RA-%s" % self.proj
ctype2 = "DEC-%s" % self.proj
crval1, crval2 = self.center.ra(), self.center.dec()
cdelt1, cdelt2 = -self.pixelsize, self.pixelsize
# from SkyImage.cxx like 92:
# "center pixel; WCS convention is that center of a pixel is a half-integer"
crpix1, crpix2 = (self.skyimage.naxis1() +
1) / 2.0, (self.skyimage.naxis2() + 1) / 2.0
values = [
["TELESCOP", "GLAST"],
["INSTRUME", "LAT"],
["DATE-OBS", ""],
["DATE-END", ""],
["EQUINOX", 2000.0, "Equinox of RA & DEC specifications"],
[
"CTYPE1", ctype1,
"[RA|GLON]---%%%, %%% represents the projection method such as AIT"
],
["CRPIX1", crpix1, "Reference pixel"],
["CRVAL1", crval1, "RA or GLON at the reference pixel"],
[
"CDELT1", cdelt1,
"X-axis incr per pixel of physical coord at position of ref pixel(deg)"
],
[
"CTYPE2", ctype2,
"[DEC|GLAT]---%%%, %%% represents the projection method such as AIT"
],
["CRPIX2", crpix2, "Reference pixel"],
["CRVAL2", crval2, "DEC or GLAT at the reference pixel"],
[
"CDELT2", cdelt2,
"Y-axis incr per pixel of physical coord at position of ref pixel(deg)"
],
["CROTA2", 0, "Image rotation (deg)"],
]
for i in values:
if len(i) > 2 and len(i[2]) > 47: i[2] = i[2][0:47]
cards = [pyfits.Card(*i) for i in values]
header = pyfits.Header(cards=cards)
hdu = pyfits.PrimaryHDU(data=self.image, header=header)
fits = pyfits.HDUList([hdu])
return fits
class ModelImage(ROIImage):
""" This ROIImage subclass fills the sky image with the model
predicted counts for a fermi sky model described by an ROIAnalysis
object.
This code is forced to deal with the fact that model intensity
can vary significantly across a spatial pixel. The rest of the
pointlike code can avoid this whole issue by scaling the healpix
pixel size with the PSF to ensure that pixels are always small
compared to the instrument's intrisic resolution. But since
model predicted counts maps can be generated of arbitary pixel size,
this issue must directly be dealt with.
The solution that this code uses to deal with this issue is to
simply sample from a grid finer by an integer number of pixels
in each dimensions. After calculating the model predictions,
the nearby blocks of model predictions are averaged to downsample
to create the model predictions. This formulation assumes that
each of the subpixels has the same solid angle and so it only
suitable for relativly small images where pixels have equal area.
For that reason, it is advised to use the ZEA projection.
For point and extended sources, the characteristic scale with
which the convolution must be small compared to is the PSF. So
the formula for determining the factor is
factor = ceil(pixelsize/r10)
Where pxielsize is the plotting pixel size and r10 is the 10%
containment radius of the PSF.
For background sources, the characteristic scale is not the PSF
but the convolution grid pixelsize. So the formula for determining
the factor is instead
factor = ceil(pixelsize/(conv_pixelsize/4))
Where conv_pixelsize is the size of the convolution grid's pixels.
For background sources, this algorithm is generally efficiency
since we except the background to vary on this smaller scale all
across the image. But for point and (small) extended sources,
this algorithm is generally very poor because it requires
calculating the PSF (or PDF) at many points where the value
is very close to 0. A better algorithm would be an adaptive
quadrature integration algorithm which evaluate the integral in
each pixel, then did a more accurate integral and iterated until
the integral converged. This would avoid having to evaluate the
model predictions for a source very finely far from the source.
On the other hand, adding this feature (presumably to C++
for optimization) would be very costly, and this code runs
fast enough...
"""
defaults = ROIImage.defaults + (
('override_point_sources', None,
""" If either is specified, use override_point_sources these
and override_diffuse_sources to generate the image instead
of the sources in the ROI."""
),
('override_diffuse_sources', None, 'Same as override_point_sources'),
)
@keyword_options.decorate(defaults)
def __init__(self, *args, **kwargs):
if kwargs.has_key('proj') and kwargs['proj'] != 'ZEA':
print "Warning, it is strongly advised to use the 'ZEA projection when creating model counts maps."
super(ModelImage, self).__init__(*args, **kwargs)
def fill(self):
self.wsdl = self.skyimage.get_wsdl()
self.solid_angle = np.radians(self.pixelsize)**2
model_counts = np.zeros(len(self.wsdl), dtype=float)
model_counts += self.all_point_source_counts()
model_counts += self.all_diffuse_sources_counts()
model_counts *= self.roi.phase_factor # don't forget about the phase factor!
#NB -- this will need to be fixed if want to account for bracketing IRFs
PythonUtilities.set_wsdl_weights(model_counts, self.wsdl)
self.skyimage.set_wsdl(self.wsdl)
@staticmethod
def downsample(myarr, factor):
"""
Code taken from http://code.google.com/p/agpy/source/browse/trunk/agpy/downsample.py
Downsample a 1D or 2D array by averaging over *factor* pixels in each axis.
Crops upper edge if the shape is not a multiple of factor.
This code is pure numpy and should be fast.
"""
assert isinstance(factor, numbers.Integral)
assert len(myarr.shape) <= 2
if len(myarr.shape) == 1:
xs = myarr.shape[0]
assert xs % factor == 0
dsarr = np.concatenate([[myarr[i::factor]]
for i in range(factor)]).mean(axis=0)
return dsarr
elif len(myarr.shape) == 2:
xs, ys = myarr.shape
assert xs % factor == 0 and ys % factor == 0
dsarr = np.concatenate(
[[myarr[i::factor, j::factor] for i in range(factor)]
for j in range(factor)]).mean(axis=0)
return dsarr
def bigger_wsdl(self, band, compare=None):
""" Want to sample on a grid that is comparable in size (or
smaller than) 10% of the psf to ensure we get a reasonable
sampling of the grid. """
if compare is None:
r10 = band.psf.inverse_integral_on_axis(0.10)
compare = r10
self.factor = int(np.ceil(self.pixelsize / compare))
if self.factor == 1:
return self.wsdl
else:
# hold onto this thing since it is needed by downsample_model
if not hasattr(self.size, '__iter__'):
self.fine_skyimage = SkyImage(
self.center, '',
float(self.pixelsize) / self.factor, self.size, 1,
self.proj, self.galactic, False)
else:
self.fine_skyimage = SkyImage(
self.center, '',
float(self.pixelsize) / self.factor, float(self.size[0]),
1, self.proj, self.galactic, False, float(self.size[1]))
wsdl = self.fine_skyimage.get_wsdl()
return wsdl
def downsample_model(self, rvals):
if self.factor == 1:
return rvals
else:
rvals = rvals.reshape(
(self.fine_skyimage.naxis2(), self.fine_skyimage.naxis1()))
rvals = ModelImage.downsample(rvals, self.factor).flatten()
return rvals
@staticmethod
def get_point_sources(roi, override_point_sources,
override_diffuse_sources):
if override_point_sources is None and override_diffuse_sources is None:
return roi.psm.point_sources
if override_point_sources is None:
return []
elif not isinstance(override_point_sources, collections.Iterable):
return [override_point_sources]
else:
return override_point_sources
def all_point_source_counts(self):
""" Calculate the point source contributions. """
point_sources = ModelImage.get_point_sources(
self.roi, self.override_point_sources,
self.override_diffuse_sources)
if len(point_sources) == 0: return 0
point_counts = np.zeros(len(self.wsdl), dtype=float)
for band in self.selected_bands:
cpsf = band.psf.cpsf
# generate a list of skydirs on a finer grid.
wsdl = self.bigger_wsdl(band)
rvals = np.empty(len(wsdl), dtype=float)
for nps, ps in enumerate(point_sources):
# evaluate the PSF at the center of each pixel
cpsf.wsdl_val(rvals, ps.skydir, wsdl)
# average the finer grid back to original resolution.
temp = self.downsample_model(rvals)
temp *= self.solid_angle #multiply by pixel solid angle
temp *= band.expected(
ps.model) # scale by total expected counts
point_counts += temp
return point_counts
def extended_source_counts(self, extended_model):
rd = self.roi.roi_dir
es = extended_model.extended_source
sm = es.smodel
extended_counts = np.zeros(len(self.wsdl), dtype=float)
for band in self.selected_bands:
extended_model.set_state(band)
exposure = band.exp.value
er = exposure(es.spatial_model.center,
extended_model.current_energy) / exposure(
rd, extended_model.current_energy)
es_counts = band.expected(sm) * er
wsdl = self.bigger_wsdl(band)
es_pix_counts = extended_model._pix_value(wsdl) * self.solid_angle
es_pix_counts = self.downsample_model(es_pix_counts)
bg_pix_counts = es_pix_counts * es_counts
extended_counts += bg_pix_counts
return extended_counts
def otf_source_counts(self, bg):
roi = self.roi
mo = bg.smodel
background_counts = np.zeros(len(self.wsdl), dtype=float)
for band in self.selected_bands:
ns, bg_points, bg_vector = ROIDiffuseModel_OTF.sub_energy_binning(
band, bg.nsimps)
pi_evals = np.empty([len(self.wsdl), ns + 1])
wsdl = self.bigger_wsdl(band, compare=bg.pixelsize / 4.0)
for ne, e in enumerate(bg_points):
bg.set_state(e, band.ct, band)
temp = self.downsample_model(bg._pix_value(wsdl))
pi_evals[:, ne] = temp
pi_evals *= (self.solid_angle * bg_vector)
mo_evals = mo(bg_points)
pi_counts = (pi_evals * mo_evals).sum(axis=1)
background_counts += pi_counts
return background_counts
def diffuse_source_counts(self, bg):
if isinstance(bg, ROIDiffuseModel_OTF):
return self.otf_source_counts(bg)
elif isinstance(bg, ROIExtendedModel):
return self.extended_source_counts(bg)
else:
raise Exception(
"Unable to calculate model predictions for diffuse source %s",
bg.name)
@staticmethod
def get_diffuse_sources(roi, override_point_sources,
override_diffuse_sources):
if override_point_sources is None and override_diffuse_sources is None:
return roi.dsm.bgmodels
else:
mapper = get_default_diffuse_mapper(roi.sa, roi.roi_dir, roi.quiet)
if override_diffuse_sources is None:
return []
elif not isinstance(override_diffuse_sources,
collections.Iterable):
return [mapper(override_diffuse_sources)]
else:
return [mapper(ds) for ds in override_diffuse_sources]
def all_diffuse_sources_counts(self):
""" Calculate the diffuse source contributions. """
bgmodels = ModelImage.get_diffuse_sources(
self.roi, self.override_point_sources,
self.override_diffuse_sources)
return sum(self.diffuse_source_counts(bg) for bg in bgmodels)