def test_fit(self):
ui.load_arrays(1, self.x, self.y)
ui.set_source("polynom1d.p")
ui.thaw("p.c1")
ui.set_method("levmar")
ui.fit()
model = ui.get_model_component("p")
expected = [0, 1]
observed = [model.c0.val, model.c1.val]
assert_almost_equal(observed, expected)
def test_fit(self):
ui.load_arrays(1, self.x, self.y)
ui.set_source("polynom1d.p")
ui.thaw("p.c1")
ui.set_method("levmar")
ui.fit()
model = ui.get_model_component("p")
expected = [0, 1]
observed = [model.c0.val, model.c1.val]
assert_almost_equal(observed, expected)
def test_fit(self):
"""
Perform a very simple fit with built-in models, and check that the results make sense.
"""
ui.load_arrays(1, self.x, self.y)
ui.set_source("polynom1d.p")
ui.thaw("p.c1")
ui.set_method("levmar")
ui.fit()
model = ui.get_model_component("p")
assert_almost_equal(model.c0.val, 0)
assert_almost_equal(model.c1.val, 1)
def test_fit(self):
"""
Perform a very simple fit with built-in models, and check that the results make sense.
"""
ui.load_arrays(1, self.x, self.y)
ui.set_source("polynom1d.p")
ui.thaw("p.c1")
ui.set_method("levmar")
ui.fit()
model = ui.get_model_component("p")
expected = [0, 1]
observed = [model.c0.val, model.c1.val]
assert_almost_equal(observed, expected)
# CHXE model
shp.set_full_model(psf(shp.gauss2d.chxe * emap) + bg * emap)
# inner radii chosen
for r in [20, 24, 28, 32]:
# from KP15, (ra, dec) = (266.4172 deg, -29.00716 deg)
# systematic shifting error = 6" = 2.4 px
# ellip = .52
# theta = 57 deg (from positive north)
shp.set_par(chxe.xpos, 497.4, 497.4 - 4, 497.4 + 4)
shp.set_par(chxe.ypos, 499.1, 499.1 - 4, 499.1 + 4)
shp.set_par(chxe.fwhm, 30, 1, 200)
shp.set_par(chxe.ellip, .5)
shp.set_par(chxe.theta, -.9948)
shp.set_par(chxe.ampl, 1e-5)
shp.thaw(chxe.ellip, chxe.xpos, chxe.ypos)
print(shp.get_model())
shp.ignore2d('circle(500,500,1000)')
shp.notice2d('circle(500,500,60)')
shp.ignore2d('circle(500,500,' + str(r) + ')')
shp.fit()
print(shp.get_model())
shp.set_conf_opt('numcores', 3)
shp.set_conf_opt('maxiters', 50)
shp.set_conf_opt('fast', True)
shp.set_conf_opt('remin', 10000.0)
shp.set_conf_opt('soft_limits', True)
yp, xp = np.unravel_index(
np.nanargmax(resid_smooth.data), resid_smooth.data.shape
)
ampl = resid_smooth.get_by_pix((xp, yp))[0]
# creates g0 as a gauss2d instance
sh.set_full_model(bkg + psf(sh.gauss2d.g0) * expo)
g0.xpos, g0.ypos = xp, yp
sh.freeze(g0.xpos, g0.ypos) # fix the position in the initial fitting step
# fix exposure amplitude so that typical exposure is of order unity
expo.ampl = 1e-9
sh.freeze(expo)
sh.thaw(g0.fwhm, g0.ampl) # in case frozen in a previous iteration
g0.fwhm = 10 # give some reasonable initial values
g0.ampl = ampl
# In[ ]:
get_ipython().run_cell_magic('time', '', 'sh.fit()')
# Fit all parameters of this Gaussian component, fix them and re-compute the residuals map.
# In[ ]:
abs1 = ui.xsphabs.abs1
pow1 = ui.powlaw1d.pow1
src_model1 = abs1 * pow1
src_models = [src_model1, src_model1 * ui.const1d.ratio_12]
vals_iter = izip(count(1), src_models, ds.get_response(), bkg_models, ds.get_bkg_scale())
for i, src_model, rsp, bkg_model, bkg_scale in vals_iter:
ds[i].set_full_model(rsp(src_model) + bkg_scale * bkg_model)
ds[i].set_bkg_full_model(bkg_model)
## Fit background
ds.notice(0.5, 8.0)
ui.set_method("neldermead")
ui.set_stat("cash")
ui.thaw(c1.c0)
ui.thaw(c2.c0)
ui.fit_bkg()
ui.freeze(c1.c0)
ui.freeze(c2.c0)
ui.set_par(abs1.nh, 0.0398)
ui.freeze(abs1)
ui.fit()
ds.plot_fit()
# ds.plot_bkg_fit()
# FIT OUTPUT:
#
# Datasets = 1, 2
# Method = neldermead
maxcoord = resid_smo6.lookup_max()
maxpix = resid_smo6.wcs_skycoord_to_pixel(maxcoord[0])
print(maxcoord)
print(maxpix)
sh.set_full_model(
bkg + psf(sh.gauss2d.g0) * expo) # creates g0 as a gauss2d instance
# In[56]:
g0.xpos = maxpix[0]
g0.ypos = maxpix[1]
sh.freeze(g0.xpos, g0.ypos)
expo.ampl = 1e-9
sh.freeze(expo)
sh.thaw(g0.fwhm, g0.ampl)
g0.fwhm = 10
g0.ampl = maxcoord[1]
sh.fit()
# In[57]:
sh.thaw(g0.xpos, g0.ypos)
sh.fit()
sh.covar()
sh.freeze(g0)
data = sh.get_data_image().y - sh.get_model_image().y
resid = SkyImage(data=data, wcs=ref_image.wcs)
resid_smo6 = resid.smooth(radius=6)
import sherpa.astro.ui as shp
shp.restore('20-40 keV/fits/chxepwnblob.sav')
shp.set_conf_opt('numcores', 3)
shp.set_conf_opt('maxiters', 50)
shp.set_conf_opt('fast', True)
shp.set_conf_opt('remin', 10000.0)
shp.set_conf_opt('soft_limits', True)
shp.set_conf_opt('verbose', True)
shp.freeze(chxe)
shp.thaw(chxe.ampl)
print(shp.get_model())
shp.conf(blob.xpos, blob.ypos, blob.ellip, blob.fwhm, blob.theta, blob.ampl)
shp.save('20-40 keV/fits/chxepwnblobconf.sav')
def fit_sherpa(obsid_list,
redshift,
nH_Gal,
energy,
min_counts=25,
kT_guess=3,
Ab_guess=1,
fix_nH_Gal=True,
fix_abund=False,
find_errors=True):
spectra = []
for obs in obsid_list:
temp = glob.glob('xaf_*_' + obs + '.pi') # get spectra of regions
spectra.append(
temp
) # spectra will be made of lists which have xaf_*_obs.pi filenames - access with spectra[i][j]
spectra.sort()
num_obs = len(obsid_list)
num_reg = len(temp)
filename = 'spectra_wabs_mekal.dat'
results_file = open(filename, "w")
results_file.write(
'# Fit results for wabs*mekal (zeros indicate that no fitting was performed)\n'
)
results_file.write(
'# Reg_no. kT kT_loerr kT_hierr Z Z_loerr Z_hierr norm norm_loerr norm_hierr nH_Gal nH_loerr nH_hierr red_chisq total_counts num_bins\n'
)
for i in range(num_reg):
sherpa.clean() # clean everything
cnts = numpy.zeros(
num_obs
) # make array of zeros with index length same as num_obs to store counts
max_rate = numpy.zeros(num_obs) # max count rate [counts/s/keV]
data_set = 0 # data set number
good_src_ids = numpy.zeros(num_obs, dtype=int) - 1
for j in range(num_obs):
sherpa.load_pha(
data_set, spectra[j]
[i]) # load xaf_#_obs_####.pi and .arf and .rmf files.
sherpa.ignore_id(data_set, 0.0, energy[0])
sherpa.ignore_id(data_set, energy[1], None)
cnts[j] = sherpa.calc_data_sum(energy[0], energy[1], data_set)
cnt_rate = sherpa.get_rate(data_set, filter=True)
if len(cnt_rate) == 0:
max_rate[
j] = 0.0 # when few counts (<50), get_rate can return zero-length array
else:
max_rate[j] = numpy.max(cnt_rate)
sherpa.subtract(data_set) # subtract background
sherpa.set_source(
data_set, sherpa.xswabs.abs1 *
sherpa.xsmekal.plsm1) # 1 temperature mekal model fit
good_src_ids[j] = data_set
data_set += 1 # same run for region but different obs
# Filter out ignored obs
good_src_ids_indx = numpy.where(good_src_ids >= 0)
good_src_ids = good_src_ids[good_src_ids_indx]
max_rate = max_rate[good_src_ids_indx]
cnts = cnts[good_src_ids_indx]
totcnts = numpy.sum(cnts)
if totcnts >= min_counts:
print('Fitting spectra in region: ' + str(i))
abs1.nH = nH_Gal
abs1.cache = 0
if fix_nH_Gal:
sherpa.freeze(abs1.nH)
else:
sherpa.thaw(abs1.nH)
plsm1.kt = kT_guess
sherpa.thaw(plsm1.kt)
plsm1.Abundanc = Ab_guess
if fix_abund:
sherpa.freeze(plsm1.Abundanc)
else:
sherpa.thaw(plsm1.Abundanc)
plsm1.redshift = redshift
sherpa.freeze(plsm1.redshift)
plsm1.cache = 0
sherpa.fit()
fit_result = sherpa.get_fit_results()
red_chi2 = fit_result.rstat
num_bins = fit_result.numpoints
if fix_nH_Gal:
nH = nH_Gal
kT = fit_result.parvals[0]
if fix_abund:
Z = Ab_guess
norm = fit_result.parvals[1]
else:
Z = fit_result.parvals[1]
norm = fit_result.parvals[2]
else:
nH = fit_result.parvals[0]
kT = fit_result.parvals[1]
if fix_abund:
Z = Ab_guess
norm = fit_result.parvals[2]
else:
Z = fit_result.parvals[2]
norm = fit_result.parvals[3]
del fit_result
if find_errors:
sherpa.covar()
covar_result = sherpa.get_covar_results()
if fix_nH_Gal:
nH_loerr = 0.0
nH_hierr = 0.0
kT_loerr = covar_result.parmins[0]
kT_hierr = covar_result.parmaxes[0]
if fix_abund:
Z_loerr = 0.0
Z_hierr = 0.0
norm_loerr = covar_result.parmins[1]
norm_hierr = covar_result.parmaxes[1]
else:
Z_loerr = covar_result.parmins[1]
Z_hierr = covar_result.parmaxes[1]
norm_loerr = covar_result.parmins[2]
norm_hierr = covar_result.parmaxes[2]
else:
nH_loerr = covar_result.parmins[0]
nH_hierr = covar_result.parmaxes[0]
kT_loerr = covar_result.parmins[1]
kT_hierr = covar_result.parmaxes[1]
if fix_abund:
Z_loerr = 0.0
Z_hierr = 0.0
norm_loerr = covar_result.parmins[2]
norm_hierr = covar_result.parmaxes[2]
else:
Z_loerr = covar_result.parmins[2]
Z_hierr = covar_result.parmaxes[2]
norm_loerr = covar_result.parmins[3]
norm_hierr = covar_result.parmaxes[3]
del covar_result
# Check for failed errors (= None) and set them to +/- best-fit value
if not fix_nH_Gal:
if nH_loerr is None: nH_loerr = -nH # is was ==
if nH_hierr is None: nH_hierr = nH
if kT_loerr is None: kT_loerr = -kT
if kT_hierr is None: kT_hierr = kT
if not fix_abund:
if Z_loerr is None: Z_loerr = -Z
if Z_hierr is None: Z_hierr = Z
if norm_loerr is None: norm_loerr = -norm
if norm_hierr is None: norm_hierr = norm
else:
kT_loerr = 0.0
Z_loerr = 0.0
nH_loerr = 0.0
norm_loerr = 0.0
kT_hierr = 0.0
Z_hierr = 0.0
nH_hierr = 0.0
norm_hierr = 0.0
else: # if total counts < min_counts, just write zeros
print('\n Warning: no fit performed for for region: ' + str(i))
print(
'\n Spectra have insufficient counts after filtering or do not exist.'
)
print('\n --> All parameters for this region set to 0.0.')
kT = 0.0
Z = 0.0
nH = 0.0
norm = 0.0
kT_loerr = 0.0
Z_loerr = 0.0
nH_loerr = 0.0
norm_loerr = 0.0
kT_hierr = 0.0
Z_hierr = 0.0
nH_hierr = 0.0
norm_hierr = 0.0
red_chi2 = 0.0
num_bins = 0
reg_id = spectra[0][i].split(
'_'
) # Splits string after every underscore so that region number can be accessed. reg_id[1] is accessed because that is the region number after 'xaf'
results_file.write(
'%7r %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %6.4e %6.4e %6.4e %7.4f %7.4f %7.4f %7.4f %8.1f %8r\n'
% (int(reg_id[1]), kT, kT_loerr, kT_hierr, Z, Z_loerr, Z_hierr,
norm, norm_loerr, norm_hierr, nH, nH_loerr, nH_hierr, red_chi2,
totcnts, num_bins)) # Write all data to a file
results_file.close()
def fit_sherpa(obsid_list, redshift, nH_Gal, energy, min_counts=25, kT_guess=3, Ab_guess=1, fix_nH_Gal=True, fix_abund=False, find_errors=True):
spectra = []
for obs in obsid_list:
temp = glob.glob('xaf_*_' + obs + '.pi') # get spectra of regions
spectra.append(temp) # spectra will be made of lists which have xaf_*_obs.pi filenames - access with spectra[i][j]
spectra.sort()
num_obs = len(obsid_list)
num_reg = len(temp)
filename = 'spectra_wabs_mekal.dat'
results_file = open(filename, "w")
results_file.write('# Fit results for wabs*mekal (zeros indicate that no fitting was performed)\n')
results_file.write('# Reg_no. kT kT_loerr kT_hierr Z Z_loerr Z_hierr norm norm_loerr norm_hierr nH_Gal nH_loerr nH_hierr red_chisq total_counts num_bins\n')
for i in range(num_reg):
sherpa.clean() # clean everything
cnts = numpy.zeros(num_obs) # make array of zeros with index length same as num_obs to store counts
max_rate = numpy.zeros(num_obs) # max count rate [counts/s/keV]
data_set = 0 # data set number
good_src_ids = numpy.zeros(num_obs, dtype=int) - 1
for j in range(num_obs):
sherpa.load_pha(data_set, spectra[j][i]) # load xaf_#_obs_####.pi and .arf and .rmf files.
sherpa.ignore_id(data_set, 0.0, energy[0])
sherpa.ignore_id(data_set, energy[1], None)
cnts[j] = sherpa.calc_data_sum(energy[0], energy[1], data_set)
cnt_rate = sherpa.get_rate(data_set, filter=True)
if len(cnt_rate) == 0:
max_rate[j] = 0.0 # when few counts (<50), get_rate can return zero-length array
else:
max_rate[j] = numpy.max(cnt_rate)
sherpa.subtract(data_set) # subtract background
sherpa.set_source(data_set, sherpa.xswabs.abs1 * sherpa.xsmekal.plsm1) # 1 temperature mekal model fit
good_src_ids[j] = data_set
data_set += 1 # same run for region but different obs
# Filter out ignored obs
good_src_ids_indx = numpy.where(good_src_ids >= 0)
good_src_ids = good_src_ids[good_src_ids_indx]
max_rate = max_rate[good_src_ids_indx]
cnts = cnts[good_src_ids_indx]
totcnts = numpy.sum(cnts)
if totcnts >= min_counts:
print('Fitting spectra in region: ' + str(i))
abs1.nH = nH_Gal
abs1.cache = 0
if fix_nH_Gal:
sherpa.freeze(abs1.nH)
else:
sherpa.thaw(abs1.nH)
plsm1.kt = kT_guess
sherpa.thaw(plsm1.kt)
plsm1.Abundanc = Ab_guess
if fix_abund:
sherpa.freeze(plsm1.Abundanc)
else:
sherpa.thaw(plsm1.Abundanc)
plsm1.redshift = redshift
sherpa.freeze(plsm1.redshift)
plsm1.cache = 0
sherpa.fit()
fit_result = sherpa.get_fit_results()
red_chi2 = fit_result.rstat
num_bins = fit_result.numpoints
if fix_nH_Gal:
nH = nH_Gal
kT = fit_result.parvals[0]
if fix_abund:
Z = Ab_guess
norm = fit_result.parvals[1]
else:
Z = fit_result.parvals[1]
norm = fit_result.parvals[2]
else:
nH = fit_result.parvals[0]
kT = fit_result.parvals[1]
if fix_abund:
Z = Ab_guess
norm = fit_result.parvals[2]
else:
Z = fit_result.parvals[2]
norm = fit_result.parvals[3]
del fit_result
if find_errors:
sherpa.covar()
covar_result = sherpa.get_covar_results()
if fix_nH_Gal:
nH_loerr = 0.0
nH_hierr = 0.0
kT_loerr = covar_result.parmins[0]
kT_hierr = covar_result.parmaxes[0]
if fix_abund:
Z_loerr = 0.0
Z_hierr = 0.0
norm_loerr = covar_result.parmins[1]
norm_hierr = covar_result.parmaxes[1]
else:
Z_loerr = covar_result.parmins[1]
Z_hierr = covar_result.parmaxes[1]
norm_loerr = covar_result.parmins[2]
norm_hierr = covar_result.parmaxes[2]
else:
nH_loerr = covar_result.parmins[0]
nH_hierr = covar_result.parmaxes[0]
kT_loerr = covar_result.parmins[1]
kT_hierr = covar_result.parmaxes[1]
if fix_abund:
Z_loerr = 0.0
Z_hierr = 0.0
norm_loerr = covar_result.parmins[2]
norm_hierr = covar_result.parmaxes[2]
else:
Z_loerr = covar_result.parmins[2]
Z_hierr = covar_result.parmaxes[2]
norm_loerr = covar_result.parmins[3]
norm_hierr = covar_result.parmaxes[3]
del covar_result
# Check for failed errors (= None) and set them to +/- best-fit value
if not fix_nH_Gal:
if nH_loerr is None: nH_loerr = -nH # is was ==
if nH_hierr is None: nH_hierr = nH
if kT_loerr is None: kT_loerr = -kT
if kT_hierr is None: kT_hierr = kT
if not fix_abund:
if Z_loerr is None: Z_loerr = -Z
if Z_hierr is None: Z_hierr = Z
if norm_loerr is None: norm_loerr = -norm
if norm_hierr is None: norm_hierr = norm
else:
kT_loerr = 0.0
Z_loerr = 0.0
nH_loerr = 0.0
norm_loerr = 0.0
kT_hierr = 0.0
Z_hierr = 0.0
nH_hierr = 0.0
norm_hierr = 0.0
else: # if total counts < min_counts, just write zeros
print('\n Warning: no fit performed for for region: ' + str(i))
print('\n Spectra have insufficient counts after filtering or do not exist.')
print('\n --> All parameters for this region set to 0.0.')
kT = 0.0
Z = 0.0
nH = 0.0
norm = 0.0
kT_loerr = 0.0
Z_loerr = 0.0
nH_loerr = 0.0
norm_loerr = 0.0
kT_hierr = 0.0
Z_hierr = 0.0
nH_hierr = 0.0
norm_hierr = 0.0
red_chi2 = 0.0
num_bins = 0
reg_id = spectra[0][i].split('_') # Splits string after every underscore so that region number can be accessed. reg_id[1] is accessed because that is the region number after 'xaf'
results_file.write('%7r %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %6.4e %6.4e %6.4e %7.4f %7.4f %7.4f %7.4f %8.1f %8r\n' % (int(reg_id[1]), kT, kT_loerr, kT_hierr, Z, Z_loerr, Z_hierr, norm, norm_loerr, norm_hierr, nH, nH_loerr, nH_hierr, red_chi2, totcnts, num_bins)) # Write all data to a file
results_file.close()